chr3:142562770:A>G Detail (hg38) (ATR)

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

Genome

Assembly	Position
hg19	chr3:142,281,612-142,281,612 View the variant detail on this assembly version.
hg38	chr3:142,562,770-142,562,770

HGVS

Type	Transcript	Protein
RefSeq	NM_001184.3:c.632T>C	NP_001175.2:p.Met211Thr
Ensemble	ENST00000350721.9:c.632T>C	ENST00000350721.9:p.Met211Thr
	ENST00000661310.1:c.632T>C	ENST00000661310.1:p.Met211Thr

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.421
	ToMMo:0.434
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.466

Prediction

ClinVar

Clinical Significance	Benign Likely benign
Review star
Show details

Links

Type	Database	ID	Link
Gene	MIM	601215	OMIM
	HGNC	882	HGNC
	Ensembl	ENSG00000175054	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv14490130	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign Likely benign	2016-03-28	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Benign	2021-07-14	criteria provided, multiple submitters, no conflicts	Seckel syndrome 1	germline	Detail
Benign	2024-02-01	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Benign	2023-07-07	criteria provided, single submitter	Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
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_001184.4(ATR):c.632T>C (p.Met211Thr) AND not specified	ClinVar	Detail
NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND Seckel syndrome 1	ClinVar	Detail
NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND not provided	ClinVar	Detail
NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND Familial cutaneous telangiectasia and oropharyngeal pred...	ClinVar	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: rs2227928 dbSNP
Genome: hg38
Position: chr3:142,562,770-142,562,770
Variant Type: snv
Reference Allele: A
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 80.48
Standard deviation of sample read depth (HGVD): 33.22
Number of reference allele (HGVD): 1401
Number of alternative allele (HGVD): 1019
Allele Frequency (HGVD): 0.42107438016528925
Gene Symbol (HGVD): ATR
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)): rs2227928
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.4339
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 7272
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8578
East Asian Allele Counts (ExAC): 3996
East Asian Heterozygous Counts (ExAC): 2106
East Asian Homozygous Counts (ExAC): 945
East Asian Allele Frequency (ExAC): 0.4658428538120774
Chromosome Counts in All Race (ExAC): 120592
Allele Counts in All Race (ExAC): 66806
Heterozygous Counts in All Race (ExAC): 28610
Homozygous Counts in All Race (ExAC): 19098
Allele Frequency in All Race (ExAC): 0.5539836805094865

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