rs12777679

Variant names:

• chr10-87853562-T-C
• rs12777679

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 0.184 in 151,160 control chromosomes in the GnomAD database, including 2,763 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 0.18 (2763 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.183 AC: 27709 AN: 151042 Hom.: 2742 Cov.: 28

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.184 AC: 27775 AN: 151160 Hom.: 2763 Cov.: 28 AF XY: 0.185 AC XY: 13664 AN XY: 73834

African (AFR) AF: 0.128 AC: 5275 AN: 41256

American (AMR) AF: 0.232 AC: 3532 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 636 AN: 3460

East Asian (EAS) AF: 0.355 AC: 1784 AN: 5022

South Asian (SAS) AF: 0.199 AC: 949 AN: 4768

European-Finnish (FIN) AF: 0.173 AC: 1805 AN: 10440

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13225 AN: 67706

Other (OTH) AF: 0.203 AC: 426 AN: 2102

Alfa AF: 0.182 Hom.: 343

Bravo AF: 0.186

Asia WGS AF: 0.291 AC: 1012 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.38
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs12777679; hg19: chr10-89613319;