rs12902616

Variant names:

• chr15-32704974-A-G
• rs12902616

Your query was ambiguous. Multiple possible variants found:

• chr15-32704974-A-G
• chr15-32704974-A-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 0.39 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.243 AC: 10089 AN: 41496

American (AMR) AF: 0.417 AC: 6364 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5178

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4296 AN: 10582

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34171 AN: 67964

Other (OTH) AF: 0.419 AC: 884 AN: 2112

Alfa AF: 0.451 Hom.: 9551

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs12902616; hg19: chr15-32997175;