rs10510452

Variant names:

• chr3-16583541-A-G
• rs10510452

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 0.218 in 152,106 control chromosomes in the GnomAD database, including 4,240 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 0.22 (4240 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.218 AC: 33106 AN: 151988 Hom.: 4240 Cov.: 31

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.218 AC: 33111 AN: 152106 Hom.: 4240 Cov.: 31 AF XY: 0.213 AC XY: 15871 AN XY: 74348

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.251

Alfa AF: 0.282 Hom.: 9220

Bravo AF: 0.210

Asia WGS AF: 0.177 AC: 616 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	7.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510452; hg19: chr3-16625048;