12-33114009-C-T

Variant names:

• chr12-33114009-C-T
• rs10506103

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 0.383 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.679 AC: 28078 AN: 41358

American (AMR) AF: 0.354 AC: 5410 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3464

East Asian (EAS) AF: 0.796 AC: 4113 AN: 5166

South Asian (SAS) AF: 0.480 AC: 2303 AN: 4800

European-Finnish (FIN) AF: 0.207 AC: 2179 AN: 10520

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14078 AN: 67912

Other (OTH) AF: 0.344 AC: 724 AN: 2102

Alfa AF: 0.328 Hom.: 1821

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10506103; hg19: chr12-33266943;