rs12761224

Variant names:

• chr10-70767761-G-T
• rs12761224

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 0.0732 in 150,982 control chromosomes in the GnomAD database, including 537 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 0.073 (537 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0996 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: 0.0733 AC: 11063 AN: 150860 Hom.: 536 Cov.: 27

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.0732 AC: 11049 AN: 150982 Hom.: 537 Cov.: 27 AF XY: 0.0726 AC XY: 5348 AN XY: 73648

African (AFR) AF: 0.0174 AC: 719 AN: 41290

American (AMR) AF: 0.0530 AC: 804 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 295 AN: 3456

East Asian (EAS) AF: 0.0919 AC: 466 AN: 5072

South Asian (SAS) AF: 0.0617 AC: 291 AN: 4720

European-Finnish (FIN) AF: 0.120 AC: 1241 AN: 10314

Middle Eastern (MID) AF: 0.108 AC: 31 AN: 286

European-Non Finnish (NFE) AF: 0.102 AC: 6880 AN: 67680

Other (OTH) AF: 0.0764 AC: 160 AN: 2094

Alfa AF: 0.0924 Hom.: 1487

Bravo AF: 0.0696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.82
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs12761224; hg19: chr10-72527517;