rs10098073

chr8-142228143-C-A

Variant summary

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

The NM_145003.5(TSNARE1):c.*11+1330G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,136 control chromosomes in the GnomAD database, including 11,163 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 0.35 (11163 hom., cov: 33)
• Consequence: TSNARE1 NM_145003.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

Genes affected

TSNARE1 (HGNC:26437): (t-SNARE domain containing 1) Predicted to enable SNAP receptor activity and SNARE binding activity. Predicted to be involved in intracellular protein transport; vesicle docking; and vesicle fusion. Predicted to be located in membrane. Predicted to be part of SNARE complex. Predicted to be active in endomembrane system. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNARE1	NM_145003.5	c.*11+1330G>T		intron_variant		ENST00000524325.6
TSNARE1	NM_001363740.2	c.*11+1330G>T		intron_variant
TSNARE1	NM_001366901.1	c.*11+1330G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSNARE1	ENST00000524325.6	c.*11+1330G>T		intron_variant		2	NM_145003.5	A2
TSNARE1	ENST00000520166.5	c.*11+1330G>T		intron_variant		1		P2
TSNARE1	ENST00000307180.4	c.*11+1330G>T		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53698 AN: 152016 Hom.: 11165 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.353 AC: 53704 AN: 152136 Hom.: 11163 Cov.: 33 AF XY: 0.349 AC XY: 25965 AN XY: 74386

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.373

Alfa AF: 0.423 Hom.: 7015

Bravo AF: 0.337

Asia WGS AF: 0.266 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098073; hg19: chr8-143309504;