rs2913737

Variant names:

• chr5-176422988-G-A
• rs2913737

Your query was ambiguous. Multiple possible variants found:

• chr5-176422988-G-A
• chr5-176422988-G-C
• chr5-176422988-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.174 in 152,112 control chromosomes in the GnomAD database, including 2,546 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 0.17 (2546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26454 AN: 151992 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.174 AC: 26474 AN: 152112 Hom.: 2546 Cov.: 32 AF XY: 0.174 AC XY: 12959 AN XY: 74356

African (AFR) AF: 0.0941 AC: 3905 AN: 41510

American (AMR) AF: 0.159 AC: 2438 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3468

East Asian (EAS) AF: 0.107 AC: 554 AN: 5166

South Asian (SAS) AF: 0.198 AC: 956 AN: 4822

European-Finnish (FIN) AF: 0.189 AC: 2002 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15531 AN: 67964

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.208 Hom.: 9716

Bravo AF: 0.170

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.97
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2913737; hg19: chr5-175849989; COSMIC: COSV60237818;