chr10-76571560-A-G

Variant names:

• chr10-76571560-A-G
• rs2637266

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 151,892 control chromosomes in the GnomAD database, including 17,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73365 AN: 151774 Hom.: 17949 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.502

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 73398 AN: 151892 Hom.: 17955 Cov.: 32 AF XY: 0.487 AC XY: 36110 AN XY: 74182

African (AFR) AF: 0.396 AC: 16386 AN: 41426

American (AMR) AF: 0.568 AC: 8663 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2472 AN: 5154

South Asian (SAS) AF: 0.564 AC: 2718 AN: 4822

European-Finnish (FIN) AF: 0.512 AC: 5388 AN: 10522

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34366 AN: 67928

Other (OTH) AF: 0.504 AC: 1062 AN: 2108

Alfa AF: 0.501 Hom.: 6044

Bravo AF: 0.483

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2637266; hg19: chr10-78331318; COSMIC: COSV60047358;