rs35775808

chr9-99463262-A-G

Variant summary

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

The ENST00000652827.1(ENSG00000237461):n.231-190T>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 0.0445 in 152,302 control chromosomes in the GnomAD database, including 212 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 0.045 (212 hom., cov: 32)
• Consequence: ENST00000652827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

Genes affected

(HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0631 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
	ENST00000652827.1	n.231-190T>C		intron_variant, non_coding_transcript_variant
STX17-DT	ENST00000655615.1	n.269-190T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6785 AN: 152184 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0445 AC: 6784 AN: 152302 Hom.: 212 Cov.: 32 AF XY: 0.0450 AC XY: 3348 AN XY: 74470

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0355

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0534 Hom.: 36

Bravo AF: 0.0410

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.0
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: rs35775808; hg19: chr9-102225544;