rs11053044

Positions:

• chr12-33999505-A-G

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 0.279 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.279

Alfa AF: 0.315 Hom.: 1034

Bravo AF: 0.260

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11053044; hg19: chr12-34152440;