rs12581494

Positions:

• chr12-50484680-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 0.867 in 152,120 control chromosomes in the GnomAD database, including 58,817 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 0.87 (58817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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: 0.868 AC: 131877 AN: 152000 Hom.: 58787 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.867 AC: 131953 AN: 152120 Hom.: 58817 Cov.: 31 AF XY: 0.866 AC XY: 64386 AN XY: 74388

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.897

Alfa AF: 0.956 Hom.: 21477

Bravo AF: 0.845

Asia WGS AF: 0.714 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12581494; hg19: chr12-50878463;