rs12761224

chr10-70767761-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;