12-33114009-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 0.383 in 151,790 control chromosomes in the GnomAD database, including 14,865 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 0.38 (14865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58076 AN: 151672 Hom.: 14851 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.383 AC: 58145 AN: 151790 Hom.: 14865 Cov.: 32 AF XY: 0.386 AC XY: 28635 AN XY: 74154

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.344

Alfa AF: 0.317 Hom.: 1647

Bravo AF: 0.410

Asia WGS AF: 0.627 AC: 2175 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.70
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506103; hg19: chr12-33266943;