rs13259717

Positions:

• chr8-16075502-C-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 0.594 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.635

Alfa AF: 0.709 Hom.: 38481

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13259717; hg19: chr8-15933011;