rs951901

Variant names:

• chr12-58004582-C-A
• rs951901

Your query was ambiguous. Multiple possible variants found:

• chr12-58004582-C-A
• chr12-58004582-C-G
• chr12-58004582-C-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 0.583 in 151,982 control chromosomes in the GnomAD database, including 26,569 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 0.58 (26569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.583 AC: 88532 AN: 151864 Hom.: 26573 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.583 AC: 88541 AN: 151982 Hom.: 26569 Cov.: 32 AF XY: 0.580 AC XY: 43056 AN XY: 74284

African (AFR) AF: 0.466 AC: 19300 AN: 41452

American (AMR) AF: 0.580 AC: 8859 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2668 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5166

South Asian (SAS) AF: 0.561 AC: 2703 AN: 4814

European-Finnish (FIN) AF: 0.603 AC: 6349 AN: 10522

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44868 AN: 67962

Other (OTH) AF: 0.650 AC: 1372 AN: 2112

Alfa AF: 0.584 Hom.: 7506

Bravo AF: 0.576

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.54
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs951901; hg19: chr12-58398365;