NM_145206.4:c.560+69719G>A

Variant names:

• chr10-112738717-G-A
• rs7086803
• NM_145206.4:c.560+69719G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_145206.4(VTI1A):​c.560+69719G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,096 control chromosomes in the GnomAD database, including 6,948 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 0.20 (6948 hom., cov: 32)
• Consequence: VTI1A NM_145206.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 43 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTI1A	NM_145206.4	c.560+69719G>A		intron_variant	Intron 7 of 7	ENST00000393077.3	NP_660207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VTI1A	ENST00000393077.3	c.560+69719G>A		intron_variant	Intron 7 of 7	2	NM_145206.4	ENSP00000376792.2
VTI1A	ENST00000705995.1	c.581+69719G>A		intron_variant	Intron 8 of 8			ENSP00000516199.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29584 AN: 151978 Hom.: 6917 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.195 AC: 29671 AN: 152096 Hom.: 6948 Cov.: 32 AF XY: 0.191 AC XY: 14223 AN XY: 74374

African (AFR) AF: 0.559 AC: 23160 AN: 41430

American (AMR) AF: 0.153 AC: 2335 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5176

South Asian (SAS) AF: 0.0655 AC: 315 AN: 4812

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0257 AC: 1750 AN: 67996

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.0902 Hom.: 6151

Bravo AF: 0.225

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		-0.013
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7086803; hg19: chr10-114498476;