2-173394711-T-C

Variant names:

• chr2-173394711-T-C
• rs11689493

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.214 AC: 8869 AN: 41498

American (AMR) AF: 0.315 AC: 4818 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1607 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5168

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4582 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25970 AN: 67970

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.364 Hom.: 20691

Bravo AF: 0.317

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs11689493; hg19: chr2-174259439;