12-33053704-T-G

Variant names:

• chr12-33053704-T-G
• rs11052413

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 0.584 in 152,068 control chromosomes in the GnomAD database, including 27,389 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 0.58 (27389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.584 AC: 88705 AN: 151950 Hom.: 27343 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.584 AC: 88809 AN: 152068 Hom.: 27389 Cov.: 32 AF XY: 0.586 AC XY: 43588 AN XY: 74338

African (AFR) AF: 0.760 AC: 31543 AN: 41488

American (AMR) AF: 0.514 AC: 7849 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1624 AN: 3466

East Asian (EAS) AF: 0.874 AC: 4518 AN: 5168

South Asian (SAS) AF: 0.605 AC: 2913 AN: 4816

European-Finnish (FIN) AF: 0.483 AC: 5103 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33459 AN: 67976

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.545 Hom.: 2964

Bravo AF: 0.594

Asia WGS AF: 0.752 AC: 2607 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.69
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11052413; hg19: chr12-33206638;