rs10506816

chr12-79531077-T-Achr12-79531077-T-C

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 0.197 in 152,160 control chromosomes in the GnomAD database, including 7,841 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 0.20 (7841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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: 0.197 AC: 29976 AN: 152042 Hom.: 7816 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.197 AC: 30041 AN: 152160 Hom.: 7841 Cov.: 32 AF XY: 0.193 AC XY: 14382 AN XY: 74408

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.0846

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0175

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0153 Hom.: 31

Bravo AF: 0.224

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.8
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506816; hg19: chr12-79924857;