rs3091312

Variant names:

• chr3-46266981-T-A
• rs3091312

Your query was ambiguous. Multiple possible variants found:

• chr3-46266981-T-A
• chr3-46266981-T-G

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 0.268 in 152,038 control chromosomes in the GnomAD database, including 5,945 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 0.27 (5945 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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: 0.268 AC: 40706 AN: 151920 Hom.: 5924 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.268 AC: 40760 AN: 152038 Hom.: 5945 Cov.: 31 AF XY: 0.274 AC XY: 20359 AN XY: 74312

African (AFR) AF: 0.215 AC: 8899 AN: 41464

American (AMR) AF: 0.313 AC: 4777 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3107 AN: 5164

South Asian (SAS) AF: 0.424 AC: 2040 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2785 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17058 AN: 67968

Other (OTH) AF: 0.295 AC: 624 AN: 2116

Alfa AF: 0.137 Hom.: 242

Bravo AF: 0.272

Asia WGS AF: 0.483 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.52
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs3091312; hg19: chr3-46308472;