rs12761224

Variant names:

• chr10-70767761-G-T
• rs12761224

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 0.0732 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.0919

Gnomad4 SAS AF: 0.0617

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0982 Hom.: 997

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12761224; hg19: chr10-72527517;