rs3181082

Variant names:

• chr1-158332703-C-T
• rs3181082

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 0.12 in 151,992 control chromosomes in the GnomAD database, including 1,448 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 0.12 (1448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.120 AC: 18263 AN: 151874 Hom.: 1449 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.120 AC: 18265 AN: 151992 Hom.: 1448 Cov.: 32 AF XY: 0.124 AC XY: 9216 AN XY: 74320

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.118

Alfa AF: 0.112 Hom.: 132

Bravo AF: 0.116

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181082; hg19: chr1-158302493;