rs315943

chr2-113136761-G-A

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 0.625 in 152,164 control chromosomes in the GnomAD database, including 30,219 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 0.62 (30219 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95006 AN: 152046 Hom.: 30183 Cov.: 34

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.625 AC: 95090 AN: 152164 Hom.: 30219 Cov.: 34 AF XY: 0.630 AC XY: 46845 AN XY: 74408

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.599

Alfa AF: 0.599 Hom.: 12998

Bravo AF: 0.625

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.24
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315943; hg19: chr2-113894338;