rs10507452

chr13-37349644-T-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 0.0305 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;