chr12-33091298-T-C

Variant names:

• chr12-33091298-T-C
• rs1008011

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 0.508 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.614 AC: 25432 AN: 41440

American (AMR) AF: 0.472 AC: 7204 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4542 AN: 5164

South Asian (SAS) AF: 0.590 AC: 2846 AN: 4822

European-Finnish (FIN) AF: 0.375 AC: 3977 AN: 10596

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30033 AN: 67958

Other (OTH) AF: 0.504 AC: 1063 AN: 2108

Alfa AF: 0.407 Hom.: 1820

Bravo AF: 0.520

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs1008011; hg19: chr12-33244232;