12-74625974-C-T

Variant names:

• chr12-74625974-C-T
• rs822814

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 0.681 in 151,644 control chromosomes in the GnomAD database, including 36,074 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 0.68 (36074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.681 AC: 103185 AN: 151528 Hom.: 36056 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.681 AC: 103240 AN: 151644 Hom.: 36074 Cov.: 32 AF XY: 0.690 AC XY: 51091 AN XY: 74082

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.684

Alfa AF: 0.671 Hom.: 4691

Bravo AF: 0.670

Asia WGS AF: 0.870 AC: 3022 AN: 3476

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	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs822814; hg19: chr12-75019754;