2-35437731-C-T

Variant names:

• chr2-35437731-C-T
• rs13402855

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 0.7 in 151,758 control chromosomes in the GnomAD database, including 37,622 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 0.70 (37622 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.700 AC: 106156 AN: 151642 Hom.: 37591 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.700 AC: 106241 AN: 151758 Hom.: 37622 Cov.: 31 AF XY: 0.707 AC XY: 52436 AN XY: 74138

African (AFR) AF: 0.723 AC: 29922 AN: 41362

American (AMR) AF: 0.764 AC: 11650 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5101 AN: 5138

South Asian (SAS) AF: 0.800 AC: 3827 AN: 4784

European-Finnish (FIN) AF: 0.670 AC: 7050 AN: 10530

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44338 AN: 67922

Other (OTH) AF: 0.697 AC: 1468 AN: 2106

Alfa AF: 0.676 Hom.: 4242

Bravo AF: 0.708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.79
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs13402855; hg19: chr2-35662797;