chr2-135885985-C-T

Variant names:

• chr2-135885985-C-T
• rs309125

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 0.493 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.564

Alfa AF: 0.391 Hom.: 6486

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309125; hg19: chr2-136643555;