12-74625974-C-T

Position:

• chr12-74625974-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 0.681 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;