chr14:20456045:A>G Detail (hg38) (APEX1)

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

Genome

Assembly	Position
hg19	chr14:20,924,204-20,924,204 View the variant detail on this assembly version.
hg38	chr14:20,456,045-20,456,045

HGVS

APEX1

Type	Transcript	Protein
RefSeq	NM_001244249.1:c.190A>G	NP_001231178.1:p.Ile64Val
	NM_001641.3:c.190A>G	NP_001632.2:p.Ile64Val
	NM_080648.2:c.190A>G	NP_542379.1:p.Ile64Val
	NM_080649.2:c.190A>G	NP_542380.1:p.Ile64Val
Ensemble	ENST00000216714.8:c.190A>G	ENST00000216714.8:p.Ile64Val
	ENST00000398030.8:c.190A>G	ENST00000398030.8:p.Ile64Val
	ENST00000555414.5:c.190A>G	ENST00000555414.5:p.Ile64Val
	ENST00000557054.1:c.27+373A>G

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.050
	ToMMo:0.047
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.051

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

APEX1

Type	Database	ID	Link
Gene	MIM	107748	OMIM
	HGNC	587	HGNC
	Ensembl	ENSG00000100823	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv50037331	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2021-06-09	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	endometrial carcinoma	Our data indicate that except for the endometrial cancer-associated APE1 variant...	BeFree	23776569	Detail
<0.001	uterine corpus cancer	Our data indicate that except for the endometrial cancer-associated APE1 variant...	BeFree	23776569	Detail
<0.001	Malignant neoplasm of endometrium	Our data indicate that except for the endometrial cancer-associated APE1 variant...	BeFree	23776569	Detail
0.002	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.156	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.005	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.004	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
<0.001	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
<0.001	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.002	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
<0.001	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.001	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.012	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail
0.004	Non-small cell lung carcinoma	Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8...	BeFree	16195237	Detail

Annotation

Annotations

Descrption	Source	Links
NM_001641.4(APEX1):c.190A>G (p.Ile64Val) AND not provided	ClinVar	Detail
Our data indicate that except for the endometrial cancer-associated APE1 variant R237C, the polymorp...	DisGeNET	Detail
Our data indicate that except for the endometrial cancer-associated APE1 variant R237C, the polymorp...	DisGeNET	Detail
Our data indicate that except for the endometrial cancer-associated APE1 variant R237C, the polymorp...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	DisGeNET	Detail
Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G...	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: rs2307486 dbSNP
Genome: hg38
Position: chr14:20,456,045-20,456,045
Variant Type: snv
Reference Allele: A
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1202
Mean of sample read depth (HGVD): 53.52
Standard deviation of sample read depth (HGVD): 28.23
Number of reference allele (HGVD): 2285
Number of alternative allele (HGVD): 119
Allele Frequency (HGVD): 0.049500831946755405
Gene Symbol (HGVD): APEX1
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)): rs2307486
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0473
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 792
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8648
East Asian Allele Counts (ExAC): 438
East Asian Heterozygous Counts (ExAC): 404
East Asian Homozygous Counts (ExAC): 17
East Asian Allele Frequency (ExAC): 0.05064754856614246
Chromosome Counts in All Race (ExAC): 121380
Allele Counts in All Race (ExAC): 788
Heterozygous Counts in All Race (ExAC): 744
Homozygous Counts in All Race (ExAC): 22
Allele Frequency in All Race (ExAC): 0.006492008568133136

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