chr2-35437731-C-T

Position:

• chr2-35437731-C-T

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 0.7 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.697

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13402855; hg19: chr2-35662797;