10-112709306-A-T

Position:

• chr10-112709306-A-T

Variant summary

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

The NM_145206.4(VTI1A):​c.560+40308A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,076 control chromosomes in the GnomAD database, including 9,335 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 0.32 (9335 hom., cov: 32)
• Consequence: VTI1A NM_145206.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

VTI1A (HGNC:17792): (vesicle transport through interaction with t-SNAREs 1A) The protein encoded by this gene is a member of the family of soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptors (SNAREs) that function in intracellular trafficking. This family member is involved in vesicular transport between endosomes and the trans-Golgi network. It is a vesicle-associated SNARE (v-SNARE) that interacts with target membrane SNAREs (t-SNAREs). Polymorphisms in this gene have been associated with binocular function, and also with susceptibility to colorectal and lung cancers. A recurrent rearrangement has been found between this gene and the transcription factor 7-like 2 (TCF7L2) gene in colorectal cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VTI1A	NM_145206.4	c.560+40308A>T		intron_variant		ENST00000393077.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VTI1A	ENST00000393077.3	c.560+40308A>T		intron_variant		2	NM_145206.4	P4
VTI1A	ENST00000432306.5	c.561-27417A>T		intron_variant		1
VTI1A	ENST00000705995.1	c.581+40308A>T		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48443 AN: 151958 Hom.: 9329 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.319 AC: 48457 AN: 152076 Hom.: 9335 Cov.: 32 AF XY: 0.319 AC XY: 23702 AN XY: 74318

Gnomad4 AFR AF: 0.0954

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.341

Alfa AF: 0.346 Hom.: 1272

Bravo AF: 0.309

Asia WGS AF: 0.290 AC: 1006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.52

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: rs11196067; hg19: chr10-114469065;