rs4752079

Variant names:

• chr10-117559349-G-A
• rs4752079

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 0.502 in 152,094 control chromosomes in the GnomAD database, including 20,712 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 0.50 (20712 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 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: 0.502 AC: 76267 AN: 151976 Hom.: 20707 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.502 AC: 76302 AN: 152094 Hom.: 20712 Cov.: 33 AF XY: 0.497 AC XY: 36922 AN XY: 74334

African (AFR) AF: 0.292 AC: 12102 AN: 41494

American (AMR) AF: 0.561 AC: 8582 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1886 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2881 AN: 5172

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4810

European-Finnish (FIN) AF: 0.519 AC: 5476 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41443 AN: 67986

Other (OTH) AF: 0.566 AC: 1194 AN: 2108

Alfa AF: 0.581 Hom.: 11963

Bravo AF: 0.505

Asia WGS AF: 0.428 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.031
DANN	Benign	0.24
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4752079; hg19: chr10-119318860;