rs10516452

Variant names:

• chr4-99708552-C-G
• rs10516452

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 0.0799 in 152,074 control chromosomes in the GnomAD database, including 833 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 0.080 (833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.0796 AC: 12096 AN: 151956 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0676

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

GnomAD4 genome AF: 0.0799 AC: 12146 AN: 152074 Hom.: 833 Cov.: 32 AF XY: 0.0798 AC XY: 5934 AN XY: 74342

African (AFR) AF: 0.162 AC: 6696 AN: 41448

American (AMR) AF: 0.124 AC: 1890 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0234 AC: 81 AN: 3468

East Asian (EAS) AF: 0.193 AC: 997 AN: 5174

South Asian (SAS) AF: 0.0446 AC: 215 AN: 4816

European-Finnish (FIN) AF: 0.0155 AC: 164 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0284 AC: 1928 AN: 67986

Other (OTH) AF: 0.0712 AC: 150 AN: 2108

Alfa AF: 0.0521 Hom.: 56

Bravo AF: 0.0914

Asia WGS AF: 0.113 AC: 392 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	1.7
DANN	Benign	0.62
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10516452; hg19: chr4-100629709;