12-33091298-T-C

Position:

• chr12-33091298-T-C

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 0.508 in 152,032 control chromosomes in the GnomAD database, including 20,669 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 0.51 (20669 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.508 AC: 77117 AN: 151914 Hom.: 20633 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.508 AC: 77208 AN: 152032 Hom.: 20669 Cov.: 32 AF XY: 0.509 AC XY: 37848 AN XY: 74334

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.504

Alfa AF: 0.398 Hom.: 1665

Bravo AF: 0.520

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008011; hg19: chr12-33244232;