rs12902616

Positions:

• chr15-32704974-A-G
• chr15-32704974-A-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 0.39 in 152,104 control chromosomes in the GnomAD database, including 12,928 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 0.39 (12928 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59217 AN: 151986 Hom.: 12920 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.390 AC: 59262 AN: 152104 Hom.: 12928 Cov.: 33 AF XY: 0.383 AC XY: 28501 AN XY: 74366

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.419

Alfa AF: 0.435 Hom.: 4770

Bravo AF: 0.389

Asia WGS AF: 0.137 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12902616; hg19: chr15-32997175;