rs951901

chr12-58004582-C-Achr12-58004582-C-Gchr12-58004582-C-T

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 0.583 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.650

Alfa AF: 0.567 Hom.: 2921

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951901; hg19: chr12-58398365;