rs10506816

Variant names:

• chr12-79531077-T-A
• rs10506816

Your query was ambiguous. Multiple possible variants found:

• chr12-79531077-T-A
• chr12-79531077-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;