rs10507551

chr13-47187748-G-Achr13-47187748-G-T

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 0.402 in 151,846 control chromosomes in the GnomAD database, including 13,338 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 0.40 (13338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.402 AC: 60984 AN: 151728 Hom.: 13341 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.402 AC: 60982 AN: 151846 Hom.: 13338 Cov.: 32 AF XY: 0.397 AC XY: 29438 AN XY: 74210

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.452

Alfa AF: 0.406 Hom.: 2317

Bravo AF: 0.396

Asia WGS AF: 0.287 AC: 996 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.32
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507551; hg19: chr13-47761883;