chr3-157068755-G-A

Variant names:

• chr3-157068755-G-A
• rs11719102

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 0.606 in 152,124 control chromosomes in the GnomAD database, including 29,148 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 0.61 (29148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 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: 0.606 AC: 92092 AN: 152006 Hom.: 29124 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.606 AC: 92148 AN: 152124 Hom.: 29148 Cov.: 33 AF XY: 0.614 AC XY: 45678 AN XY: 74364

African (AFR) AF: 0.412 AC: 17088 AN: 41484

American (AMR) AF: 0.717 AC: 10958 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3874 AN: 5166

South Asian (SAS) AF: 0.779 AC: 3762 AN: 4828

European-Finnish (FIN) AF: 0.677 AC: 7166 AN: 10582

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44813 AN: 67988

Other (OTH) AF: 0.633 AC: 1334 AN: 2108

Alfa AF: 0.641 Hom.: 59447

Bravo AF: 0.598

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs11719102; hg19: chr3-156786544;