rs13259717

Variant names:

• chr8-16075502-C-T
• rs13259717

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 0.594 in 151,988 control chromosomes in the GnomAD database, including 29,874 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 0.59 (29874 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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: 0.594 AC: 90218 AN: 151868 Hom.: 29874 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.594 AC: 90229 AN: 151988 Hom.: 29874 Cov.: 33 AF XY: 0.594 AC XY: 44120 AN XY: 74298

African (AFR) AF: 0.283 AC: 11710 AN: 41418

American (AMR) AF: 0.561 AC: 8560 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2605 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5152

South Asian (SAS) AF: 0.606 AC: 2929 AN: 4830

European-Finnish (FIN) AF: 0.745 AC: 7853 AN: 10544

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.753 AC: 51187 AN: 67994

Other (OTH) AF: 0.635 AC: 1338 AN: 2108

Alfa AF: 0.705 Hom.: 45716

Bravo AF: 0.566

Asia WGS AF: 0.617 AC: 2144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.71
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs13259717; hg19: chr8-15933011;