GeneBe

rs1047468

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_145206.4(VTI1A):​c.*1611C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

VTI1A
NM_145206.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

Publications

7 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145206.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VTI1A
NM_145206.4
MANE Select
c.*1611C>A
3_prime_UTR
Exon 8 of 8NP_660207.2Q96AJ9-2
VTI1A
NM_001318203.2
c.*1611C>A
3_prime_UTR
Exon 9 of 9NP_001305132.1A0A994J5N6
VTI1A
NM_001365712.1
c.*1712C>A
3_prime_UTR
Exon 9 of 9NP_001352641.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VTI1A
ENST00000393077.3
TSL:2 MANE Select
c.*1611C>A
3_prime_UTR
Exon 8 of 8ENSP00000376792.2Q96AJ9-2
VTI1A
ENST00000705995.1
c.*1611C>A
3_prime_UTR
Exon 9 of 9ENSP00000516199.1A0A994J5N6
VTI1A
ENST00000876660.1
c.*1611C>A
3_prime_UTR
Exon 7 of 7ENSP00000546719.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
79606
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
36626
African (AFR)
AF:
0.00
AC:
0
AN:
3826
American (AMR)
AF:
0.00
AC:
0
AN:
2458
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
5044
East Asian (EAS)
AF:
0.00
AC:
0
AN:
11186
South Asian (SAS)
AF:
0.00
AC:
0
AN:
692
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
66
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
488
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
49176
Other (OTH)
AF:
0.00
AC:
0
AN:
6670
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
8235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.1
DANN
Benign
0.74
PhyloP100
0.048
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

Other links and lift over

dbSNP: rs1047468; hg19: chr10-114576753; API