rs12937472

Variant names:

• chr17-15350248-G-A
• rs12937472

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 0.0501 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0120 AC: 499 AN: 41526

American (AMR) AF: 0.0389 AC: 594 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0586 AC: 203 AN: 3464

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5172

South Asian (SAS) AF: 0.120 AC: 578 AN: 4804

European-Finnish (FIN) AF: 0.0548 AC: 579 AN: 10572

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0575 AC: 3907 AN: 67984

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0555 Hom.: 441

Bravo AF: 0.0473

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs12937472; hg19: chr17-15253565;