rs3181259

Variant names:

• chr11-118343352-G-A
• rs3181259

Your query was ambiguous. Multiple possible variants found:

• chr11-118343352-G-A
• chr11-118343352-G-T

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 0.176 in 152,154 control chromosomes in the GnomAD database, including 2,875 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 0.18 (2875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.176 AC: 26801 AN: 152036 Hom.: 2881 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.176 AC: 26818 AN: 152154 Hom.: 2875 Cov.: 32 AF XY: 0.185 AC XY: 13735 AN XY: 74382

African (AFR) AF: 0.154 AC: 6375 AN: 41510

American (AMR) AF: 0.121 AC: 1845 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2512 AN: 5184

South Asian (SAS) AF: 0.467 AC: 2255 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10572

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10492 AN: 67998

Other (OTH) AF: 0.169 AC: 357 AN: 2114

Alfa AF: 0.160 Hom.: 312

Bravo AF: 0.164

Asia WGS AF: 0.441 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3181259; hg19: chr11-118214067;