rs10819699

Variant names:

• chr9-99870872-A-G
• rs10819699
• ENST00000655615.1:n.178+24008T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655615.1(STX17-DT):​n.178+24008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,884 control chromosomes in the GnomAD database, including 29,446 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 0.61 (29446 hom., cov: 31)
• Consequence: STX17-DT ENST00000655615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

STX17-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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
STX17-DT	ENST00000655615.1	n.178+24008T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93257 AN: 151766 Hom.: 29407 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.615 AC: 93348 AN: 151884 Hom.: 29446 Cov.: 31 AF XY: 0.605 AC XY: 44915 AN XY: 74190

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.639

Alfa AF: 0.661 Hom.: 12976

Bravo AF: 0.619

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10819699; hg19: chr9-102633154;