rs12452417

Variant names:

• chr17-58289841-G-A
• rs12452417

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 0.127 in 152,222 control chromosomes in the GnomAD database, including 1,391 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 0.13 (1391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.159 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: 0.127 AC: 19288 AN: 152104 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.127 AC: 19288 AN: 152222 Hom.: 1391 Cov.: 32 AF XY: 0.124 AC XY: 9259 AN XY: 74426

African (AFR) AF: 0.0804 AC: 3341 AN: 41538

American (AMR) AF: 0.137 AC: 2096 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4828

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10590

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10951 AN: 68002

Other (OTH) AF: 0.155 AC: 328 AN: 2114

Alfa AF: 0.153 Hom.: 3145

Bravo AF: 0.127

Asia WGS AF: 0.0250 AC: 89 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	1.2
DANN	Benign	0.40
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs12452417; hg19: chr17-56367202;