chr10-12876764-C-T

Variant names:

• chr10-12876764-C-T
• rs7909670

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 0.518 in 151,962 control chromosomes in the GnomAD database, including 21,623 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 0.52 (21623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78661 AN: 151844 Hom.: 21603 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.518 AC: 78727 AN: 151962 Hom.: 21623 Cov.: 32 AF XY: 0.518 AC XY: 38458 AN XY: 74280

African (AFR) AF: 0.721 AC: 29909 AN: 41458

American (AMR) AF: 0.395 AC: 6036 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1859 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2340 AN: 5158

South Asian (SAS) AF: 0.490 AC: 2358 AN: 4814

European-Finnish (FIN) AF: 0.478 AC: 5033 AN: 10526

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29746 AN: 67938

Other (OTH) AF: 0.487 AC: 1027 AN: 2110

Alfa AF: 0.462 Hom.: 59201

Bravo AF: 0.521

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.28
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7909670; hg19: chr10-12918764;