rs58938945

Variant names:

• chr2-138641784-A-G
• rs58938945

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 0.517 in 152,004 control chromosomes in the GnomAD database, including 24,118 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 0.52 (24118 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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: 0.518 AC: 78628 AN: 151884 Hom.: 24110 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.517 AC: 78647 AN: 152004 Hom.: 24118 Cov.: 31 AF XY: 0.515 AC XY: 38230 AN XY: 74282

African (AFR) AF: 0.180 AC: 7480 AN: 41480

American (AMR) AF: 0.479 AC: 7315 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2706 AN: 5142

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4814

European-Finnish (FIN) AF: 0.673 AC: 7101 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47508 AN: 67966

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.612 Hom.: 44714

Bravo AF: 0.485

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.42
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs58938945; hg19: chr2-139399354;