12-50052620-C-T

Variant names:

• chr12-50052620-C-T
• rs685012

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 0.658 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.674

Alfa AF: 0.640 Hom.: 5114

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs685012; hg19: chr12-50446403;