rs10507551

Variant names:

• chr13-47187748-G-A
• rs10507551

Your query was ambiguous. Multiple possible variants found:

• chr13-47187748-G-A
• chr13-47187748-G-T

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 0.402 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.247 AC: 10213 AN: 41408

American (AMR) AF: 0.404 AC: 6158 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3472

East Asian (EAS) AF: 0.163 AC: 838 AN: 5154

South Asian (SAS) AF: 0.411 AC: 1981 AN: 4816

European-Finnish (FIN) AF: 0.397 AC: 4182 AN: 10536

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34325 AN: 67908

Other (OTH) AF: 0.452 AC: 956 AN: 2114

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10507551; hg19: chr13-47761883;