rs10507452

Variant names:

• chr13-37349644-T-G
• rs10507452

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 0.0305 in 152,226 control chromosomes in the GnomAD database, including 159 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 0.031 (159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0729 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: 0.0305 AC: 4633 AN: 152108 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0174

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00392

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0305 AC: 4647 AN: 152226 Hom.: 159 Cov.: 32 AF XY: 0.0313 AC XY: 2330 AN XY: 74432

Gnomad4 AFR AF: 0.0751

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.00393

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0106 Hom.: 53

Bravo AF: 0.0314

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
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: rs10507452; hg19: chr13-37923781;