rs12937472

Variant names:

• chr17-15350248-G-A
• rs12937472

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 0.0501 in 152,100 control chromosomes in the GnomAD database, including 324 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 0.050 (324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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 = 0.191 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: 0.0501 AC: 7620 AN: 151982 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0501 AC: 7614 AN: 152100 Hom.: 324 Cov.: 32 AF XY: 0.0523 AC XY: 3888 AN XY: 74348

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0586

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0578 Hom.: 377

Bravo AF: 0.0473

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12937472; hg19: chr17-15253565;