rs10819699

chr9-99870872-A-G

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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

STX17-DT (HGNC:51174): (STX17 divergent transcript)

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX17-DT	ENST00000655615.1	n.178+24008T>C		intron_variant, non_coding_transcript_variant

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;