17-43015940-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006373.4(VAT1):​c.*121G>C 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: 27)

Consequence

VAT1
NM_006373.4 3_prime_UTR

Scores

2
Splicing: ADA: 0.004910
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.706
Variant links:
Genes affected
VAT1 (HGNC:16919): (vesicle amine transport 1) Synaptic vesicles are responsible for regulating the storage and release of neurotransmitters in the nerve terminal. The protein encoded by this gene is an abundant integral membrane protein of cholinergic synaptic vesicles and is thought to be involved in vesicular transport. It belongs to the quinone oxidoreductase subfamily of zinc-containing alcohol dehydrogenase proteins. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VAT1NM_006373.4 linkc.*121G>C 3_prime_UTR_variant 6/6 ENST00000355653.8 NP_006364.2 Q99536-1A0A024R1Z6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VAT1ENST00000355653.8 linkc.*121G>C 3_prime_UTR_variant 6/61 NM_006373.4 ENSP00000347872.2 Q99536-1
VAT1ENST00000587173.5 linkc.*121G>C 3_prime_UTR_variant 6/62 ENSP00000465946.1 Q99536-3
VAT1ENST00000420567.7 linkc.*121G>C 3_prime_UTR_variant 6/62 ENSP00000408553.2 Q99536-2
VAT1ENST00000592388.1 linkn.*120+1G>C splice_donor_variant, intron_variant 5 ENSP00000465239.1 K7EJM4

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
Cov.:
13
GnomAD4 genome
Cov.:
27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
14
DANN
Benign
0.72
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0049
dbscSNV1_RF
Benign
0.012
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs455055; hg19: chr17-41167957; API