rs1031111

Positions:

• chr9-99399516-T-C

Variant summary

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

The XR_001746548.2(LOC107987011):​n.748A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,050 control chromosomes in the GnomAD database, including 15,461 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 0.44 (15461 hom., cov: 32)
• Consequence: LOC107987011 XR_001746548.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

LOC107987011 (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 = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987011	XR_001746548.2	n.748A>G		non_coding_transcript_exon_variant	3/4
LOC107987011	XR_007061697.1	n.2282A>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652827.1	n.487+23A>G		intron_variant, non_coding_transcript_variant
STX17-DT	ENST00000655615.1	n.419+23A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67394 AN: 151932 Hom.: 15464 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.443 AC: 67421 AN: 152050 Hom.: 15461 Cov.: 32 AF XY: 0.440 AC XY: 32688 AN XY: 74342

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.410

Alfa AF: 0.472 Hom.: 2156

Bravo AF: 0.429

Asia WGS AF: 0.289 AC: 1007 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	4.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031111; hg19: chr9-102161798;