rs11689493

chr2-173394711-T-Cchr2-173394711-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.332 in 152,074 control chromosomes in the GnomAD database, including 8,929 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 0.33 (8929 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 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: 0.332 AC: 50470 AN: 151954 Hom.: 8925 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.332 AC: 50507 AN: 152074 Hom.: 8929 Cov.: 31 AF XY: 0.334 AC XY: 24811 AN XY: 74332

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.341

Alfa AF: 0.370 Hom.: 15452

Bravo AF: 0.317

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	15
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11689493; hg19: chr2-174259439;