rs12715106

Variant names:

• chr3-26737791-G-A
• rs12715106

Your query was ambiguous. Multiple possible variants found:

• chr3-26737791-G-A
• chr3-26737791-G-T

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 0.189 in 151,742 control chromosomes in the GnomAD database, including 3,017 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 0.19 (3017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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 = 0.26 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: 0.189 AC: 28726 AN: 151622 Hom.: 3012 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.189 AC: 28735 AN: 151742 Hom.: 3017 Cov.: 32 AF XY: 0.190 AC XY: 14052 AN XY: 74114

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.202

Alfa AF: 0.195 Hom.: 400

Bravo AF: 0.183

Asia WGS AF: 0.225 AC: 780 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12715106; hg19: chr3-26779282;