rs4752923

Variant names:

• chr11-48266603-A-G
• rs4752923

Your query was ambiguous. Multiple possible variants found:

• chr11-48266603-A-G
• chr11-48266603-A-T

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 0.69 in 151,964 control chromosomes in the GnomAD database, including 36,929 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 0.69 (36929 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 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: 0.690 AC: 104762 AN: 151846 Hom.: 36916 Cov.: 30

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.690 AC: 104813 AN: 151964 Hom.: 36929 Cov.: 30 AF XY: 0.689 AC XY: 51197 AN XY: 74302

African (AFR) AF: 0.559 AC: 23158 AN: 41428

American (AMR) AF: 0.738 AC: 11255 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3466

East Asian (EAS) AF: 0.577 AC: 2972 AN: 5148

South Asian (SAS) AF: 0.544 AC: 2614 AN: 4802

European-Finnish (FIN) AF: 0.811 AC: 8576 AN: 10578

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51438 AN: 67964

Other (OTH) AF: 0.680 AC: 1438 AN: 2116

Alfa AF: 0.671 Hom.: 2583

Bravo AF: 0.682

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.84
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4752923; hg19: chr11-48288155;