rs11719102

Positions:

• chr3-157068755-G-A

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 0.606 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.633

Alfa AF: 0.661 Hom.: 16503

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11719102; hg19: chr3-156786544;