12-33999505-A-G

Variant names:

• chr12-33999505-A-G
• rs11053044

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 0.279 in 152,098 control chromosomes in the GnomAD database, including 7,487 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 0.28 (7487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42485 AN: 151980 Hom.: 7484 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.279 AC: 42488 AN: 152098 Hom.: 7487 Cov.: 32 AF XY: 0.280 AC XY: 20798 AN XY: 74344

African (AFR) AF: 0.0863 AC: 3585 AN: 41526

American (AMR) AF: 0.273 AC: 4171 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3472

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5178

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4815 AN: 10546

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26309 AN: 67962

Other (OTH) AF: 0.279 AC: 588 AN: 2110

Alfa AF: 0.306 Hom.: 1038

Bravo AF: 0.260

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11053044; hg19: chr12-34152440;