rs10516452

Positions:

• chr4-99708552-C-G

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 0.0799 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0446

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0712

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516452; hg19: chr4-100629709;