rs934299

Variant names:

• chr2-136581370-G-T
• rs934299

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.143

Alfa AF: 0.129 Hom.: 1642

Bravo AF: 0.127

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934299; hg19: chr2-137338940;