11-33830926-G-A

Variant names:

• chr11-33830926-G-A
• rs4756052

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 0.238 in 152,160 control chromosomes in the GnomAD database, including 5,699 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 0.24 (5699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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 = 0.335 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: 0.238 AC: 36187 AN: 152042 Hom.: 5703 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.00403

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.238 AC: 36172 AN: 152160 Hom.: 5699 Cov.: 32 AF XY: 0.231 AC XY: 17167 AN XY: 74390

African (AFR) AF: 0.0688 AC: 2858 AN: 41530

American (AMR) AF: 0.253 AC: 3863 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3472

East Asian (EAS) AF: 0.00404 AC: 21 AN: 5194

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4810

European-Finnish (FIN) AF: 0.233 AC: 2467 AN: 10578

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 23005 AN: 67972

Other (OTH) AF: 0.302 AC: 637 AN: 2112

Alfa AF: 0.293 Hom.: 3542

Bravo AF: 0.234

Asia WGS AF: 0.105 AC: 368 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	0.99
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4756052; hg19: chr11-33852472;