rs315943

Variant names:

• chr2-113136761-G-A
• rs315943

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;