rs309125

Variant names:

• chr2-135885985-C-T
• rs309125

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 0.493 in 152,062 control chromosomes in the GnomAD database, including 22,409 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 0.49 (22409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.493 AC: 74938 AN: 151944 Hom.: 22384 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.493 AC: 75014 AN: 152062 Hom.: 22409 Cov.: 31 AF XY: 0.502 AC XY: 37325 AN XY: 74322

African (AFR) AF: 0.762 AC: 31612 AN: 41484

American (AMR) AF: 0.605 AC: 9239 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2543 AN: 3462

East Asian (EAS) AF: 0.638 AC: 3296 AN: 5166

South Asian (SAS) AF: 0.661 AC: 3183 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10562

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20327 AN: 67980

Other (OTH) AF: 0.564 AC: 1189 AN: 2108

Alfa AF: 0.416 Hom.: 11043

Bravo AF: 0.524

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.55
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs309125; hg19: chr2-136643555;