rs4752079

chr10-117559349-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.566

Alfa AF: 0.568 Hom.: 6392

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4752079; hg19: chr10-119318860;