rs4752182

Variant names:

• chr10-118637619-A-G
• rs4752182

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 0.561 in 152,046 control chromosomes in the GnomAD database, including 24,132 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 0.56 (24132 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.561 AC: 85272 AN: 151926 Hom.: 24133 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.561 AC: 85298 AN: 152046 Hom.: 24132 Cov.: 32 AF XY: 0.564 AC XY: 41930 AN XY: 74312

African (AFR) AF: 0.531 AC: 22022 AN: 41456

American (AMR) AF: 0.532 AC: 8136 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4404 AN: 5156

South Asian (SAS) AF: 0.533 AC: 2565 AN: 4816

European-Finnish (FIN) AF: 0.610 AC: 6446 AN: 10574

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38063 AN: 67980

Other (OTH) AF: 0.558 AC: 1177 AN: 2108

Alfa AF: 0.561 Hom.: 4867

Bravo AF: 0.561

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs4752182; hg19: chr10-120397131;