chr17:30117165:A>C Detail (hg38) (NSRP1, MIR423, LOC126862529)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr17:28,444,183-28,444,183 View the variant detail on this assembly version.
hg38	chr17:30,117,165-30,117,165

HGVS

NSRP1

Type	Transcript	Protein
RefSeq	NM_032141.3:c.20+302A>C
	NM_001261467.1:c.-49+302A>C
Ensemble	ENST00000247026.10:c.20+302A>C
	ENST00000479218.6:c.21-137A>C
	ENST00000584423.5:c.20+302A>C
	ENST00000612959.4:c.-49+302A>C

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.811
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.792

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

NSRP1

Type	Database	ID	Link
Gene	MIM	616173	OMIM
	HGNC	25305	HGNC
	Ensembl	ENSG00000126653	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv57462540	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2019-01-10	criteria provided, single submitter	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	Non-small cell lung carcinoma	Five SNPs found in pre-miRNAs (rs11614913/miR-196a2, rs2910164/miR-146a, rs65051...	BeFree	22818121	Detail
0.002	breast carcinoma	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
0.001	breast carcinoma	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
0.002	Malignant neoplasm of breast	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
<0.001	Malignant neoplasm of breast	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
0.008	Malignant neoplasm of breast	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
0.001	Malignant neoplasm of breast	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
0.004	breast carcinoma	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
<0.001	breast carcinoma	However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-37...	BeFree	23982873	Detail
<0.001	Squamous cell carcinoma of esophagus	These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T...	BeFree	24260422	Detail
<0.001	esophageal carcinoma	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
0.003	Malignant neoplasm of esophagus	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
<0.001	Esophageal Neoplasms	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
0.120	Squamous cell carcinoma of esophagus	These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T...	BeFree	24260422	Detail
<0.001	Malignant neoplasm of esophagus	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
<0.001	esophageal carcinoma	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
<0.001	Esophageal Neoplasms	Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms ar...	BeFree	24260422	Detail
0.029	breast carcinoma	Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114...	BeFree	25663458	Detail
0.240	Malignant neoplasm of breast	Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114...	BeFree	25663458	Detail
0.036	Malignant neoplasm of breast	Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114...	BeFree	25663458	Detail
0.080	breast carcinoma	Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114...	BeFree	25663458	Detail
<0.001	Carcinogenesis	Taken together, these results suggest that the SNP rs6505162 in pre-miR-423 affe...	BeFree	25663458	Detail
0.080	ovarian carcinoma	Based on Cox regression and Kaplan-Meier analyses, statistically significant dif...	BeFree	19950226	Detail
0.280	Malignant neoplasm of ovary	Based on Cox regression and Kaplan-Meier analyses, statistically significant dif...	BeFree	19950226	Detail

Annotation

Annotations

Descrption	Source	Links
NM_032141.4(NSRP1):c.20+302A>C AND not provided	ClinVar	Detail
Five SNPs found in pre-miRNAs (rs11614913/miR-196a2, rs2910164/miR-146a, rs6505162/miR-423, rs228903...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
However, for the miR-146a rs2910164 (G>C), miR-149 rs2292832 (G>T), miR-373 rs12983273 (C>T...	DisGeNET	Detail
These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T>C and hsa-miR-42...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T>C and hsa-miR-42...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A polymorphisms are associated with th...	DisGeNET	Detail
Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114) of tumors underwen...	DisGeNET	Detail
Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114) of tumors underwen...	DisGeNET	Detail
Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114) of tumors underwen...	DisGeNET	Detail
Our data showed that two out of five breast cancer cell lines and 8.77 % (10/114) of tumors underwen...	DisGeNET	Detail
Taken together, these results suggest that the SNP rs6505162 in pre-miR-423 affects the mature miR e...	DisGeNET	Detail
Based on Cox regression and Kaplan-Meier analyses, statistically significant differences were noted ...	DisGeNET	Detail
Based on Cox regression and Kaplan-Meier analyses, statistically significant differences were noted ...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs6505162 dbSNP
Genome: hg38
Position: chr17:30,117,165-30,117,165
Variant Type: snv
Reference Allele: A
Alternative Allele: C
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs6505162
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.8109
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 13591
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 1794
East Asian Allele Counts (ExAC): 1420
East Asian Heterozygous Counts (ExAC): 324
East Asian Homozygous Counts (ExAC): 548
East Asian Allele Frequency (ExAC): 0.7915273132664437
Chromosome Counts in All Race (ExAC): 30244
Allele Counts in All Race (ExAC): 15979
Heterozygous Counts in All Race (ExAC): 8013
Homozygous Counts in All Race (ExAC): 3983
Allele Frequency in All Race (ExAC): 0.5283361989154873

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