rs12686676

Positions:

• chr9-99870211-A-G
• chr9-99870211-A-T

Variant summary

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

The ENST00000655615.1(STX17-DT):​n.178+24669T>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 0.452 in 151,948 control chromosomes in the GnomAD database, including 16,673 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 0.45 (16673 hom., cov: 30)
• Consequence: STX17-DT ENST00000655615.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX17-DT	ENST00000655615.1	n.178+24669T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68669 AN: 151830 Hom.: 16666 Cov.: 30

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.452 AC: 68688 AN: 151948 Hom.: 16673 Cov.: 30 AF XY: 0.443 AC XY: 32905 AN XY: 74252

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.486

Alfa AF: 0.373 Hom.: 1081

Bravo AF: 0.448

Asia WGS AF: 0.324 AC: 1129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12686676; hg19: chr9-102632493;