rs315943

Variant names:

• chr2-113136761-G-A
• rs315943

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 0.625 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.617 AC: 25596 AN: 41482

American (AMR) AF: 0.678 AC: 10366 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4769 AN: 5196

South Asian (SAS) AF: 0.517 AC: 2489 AN: 4818

European-Finnish (FIN) AF: 0.703 AC: 7443 AN: 10594

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40675 AN: 67998

Other (OTH) AF: 0.599 AC: 1267 AN: 2116

Alfa AF: 0.599 Hom.: 14526

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs315943; hg19: chr2-113894338;