rs12581494

Variant names:

• chr12-50484680-C-T
• rs12581494

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 0.867 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.684 AC: 28336 AN: 41442

American (AMR) AF: 0.843 AC: 12887 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3417 AN: 3472

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5160

South Asian (SAS) AF: 0.848 AC: 4086 AN: 4820

European-Finnish (FIN) AF: 0.960 AC: 10179 AN: 10608

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67079 AN: 68012

Other (OTH) AF: 0.897 AC: 1894 AN: 2112

Alfa AF: 0.962 Hom.: 35694

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs12581494; hg19: chr12-50878463;