rs3181096

Variant names:

• chr2-203705369-C-T
• rs3181096

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 0.345 in 151,896 control chromosomes in the GnomAD database, including 9,222 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 0.35 (9222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.587 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: 0.345 AC: 52426 AN: 151776 Hom.: 9223 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.345 AC: 52433 AN: 151896 Hom.: 9222 Cov.: 31 AF XY: 0.346 AC XY: 25696 AN XY: 74238

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.338

Alfa AF: 0.359 Hom.: 20880

Bravo AF: 0.338

Asia WGS AF: 0.450 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181096; hg19: chr2-204570092;