10-76571560-A-G

Variant names:

• chr10-76571560-A-G
• rs2637266

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.504

Alfa AF: 0.504 Hom.: 2889

Bravo AF: 0.483

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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