rs10510452

Variant names:

• chr3-16583541-A-G
• rs10510452

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 0.218 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0949 AC: 3939 AN: 41508

American (AMR) AF: 0.207 AC: 3164 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3464

East Asian (EAS) AF: 0.103 AC: 533 AN: 5172

South Asian (SAS) AF: 0.233 AC: 1122 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20433 AN: 67972

Other (OTH) AF: 0.251 AC: 530 AN: 2112

Alfa AF: 0.270 Hom.: 20716

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10510452; hg19: chr3-16625048;