rs11691765

chr2-173656446-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 0.496 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;