rs11691765

Variant names:

• chr2-173656446-G-A
• rs11691765

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 0.496 in 152,126 control chromosomes in the GnomAD database, including 22,672 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 0.50 (22672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.496 AC: 75395 AN: 152004 Hom.: 22670 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.496 AC: 75409 AN: 152126 Hom.: 22672 Cov.: 33 AF XY: 0.493 AC XY: 36705 AN XY: 74388

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.519

Alfa AF: 0.618 Hom.: 13907

Bravo AF: 0.479

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11691765; hg19: chr2-174521174;