rs12917429

Variant names:

• chr15-84881866-G-T
• rs12917429

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 0.159 in 152,226 control chromosomes in the GnomAD database, including 2,518 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 0.16 (2518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 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: 0.160 AC: 24294 AN: 152108 Hom.: 2523 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.159 AC: 24279 AN: 152226 Hom.: 2518 Cov.: 32 AF XY: 0.160 AC XY: 11902 AN XY: 74432

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.176

Alfa AF: 0.207 Hom.: 3498

Bravo AF: 0.152

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12917429; hg19: chr15-85425097;