12-50052620-C-T

Variant names:

• chr12-50052620-C-T
• rs685012

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 0.658 in 151,940 control chromosomes in the GnomAD database, including 33,140 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 0.66 (33140 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.658 AC: 99854 AN: 151820 Hom.: 33116 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.658 AC: 99926 AN: 151940 Hom.: 33140 Cov.: 31 AF XY: 0.663 AC XY: 49220 AN XY: 74274

African (AFR) AF: 0.618 AC: 25577 AN: 41390

American (AMR) AF: 0.710 AC: 10842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2725 AN: 3466

East Asian (EAS) AF: 0.841 AC: 4335 AN: 5154

South Asian (SAS) AF: 0.590 AC: 2836 AN: 4806

European-Finnish (FIN) AF: 0.722 AC: 7634 AN: 10578

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43681 AN: 67954

Other (OTH) AF: 0.674 AC: 1423 AN: 2110

Alfa AF: 0.639 Hom.: 5268

Bravo AF: 0.658

Asia WGS AF: 0.692 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.52
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs685012; hg19: chr12-50446403;