rs4758562

Variant names:

• chr11-2942440-G-A
• rs4758562

Your query was ambiguous. Multiple possible variants found:

• chr11-2942440-G-A
• chr11-2942440-G-C

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 0.838 in 152,244 control chromosomes in the GnomAD database, including 53,825 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 0.84 (53825 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 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: 0.837 AC: 127402 AN: 152126 Hom.: 53771 Cov.: 33

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.838 AC: 127515 AN: 152244 Hom.: 53825 Cov.: 33 AF XY: 0.838 AC XY: 62386 AN XY: 74416

African (AFR) AF: 0.933 AC: 38762 AN: 41544

American (AMR) AF: 0.874 AC: 13374 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2831 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4717 AN: 5188

South Asian (SAS) AF: 0.887 AC: 4278 AN: 4824

European-Finnish (FIN) AF: 0.752 AC: 7964 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52746 AN: 68006

Other (OTH) AF: 0.844 AC: 1785 AN: 2114

Alfa AF: 0.782 Hom.: 7464

Bravo AF: 0.850

Asia WGS AF: 0.896 AC: 3114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.59
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs4758562; hg19: chr11-2963670;