rs934299

Variant names:

• chr2-136581370-G-T
• rs934299

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 0.134 in 152,076 control chromosomes in the GnomAD database, including 1,413 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 0.13 (1413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.134 AC: 20404 AN: 151956 Hom.: 1411 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.134 AC: 20426 AN: 152076 Hom.: 1413 Cov.: 32 AF XY: 0.136 AC XY: 10139 AN XY: 74342

African (AFR) AF: 0.136 AC: 5633 AN: 41416

American (AMR) AF: 0.121 AC: 1849 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5170

South Asian (SAS) AF: 0.196 AC: 944 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1713 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8975 AN: 68006

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.131 Hom.: 2684

Bravo AF: 0.127

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs934299; hg19: chr2-137338940;