7-93994238-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005868.6(BET1):c.349C>G(p.Leu117Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000436 in 1,604,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
BET1
NM_005868.6 missense
NM_005868.6 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 3.85
Publications
0 publications found
Genes affected
BET1 (HGNC:14562): (Bet1 golgi vesicular membrane trafficking protein) This gene encodes a golgi-associated membrane protein that participates in vesicular transport from the endoplasmic reticulum (ER) to the Golgi complex. The encoded protein functions as a soluble N-ethylaleimide-sensitive factor attachment protein receptor and may be involved in the docking of ER-derived vesicles with the cis-Golgi membrane. 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: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15753525).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BET1 | NM_005868.6 | c.349C>G | p.Leu117Val | missense_variant | Exon 4 of 4 | ENST00000222547.8 | NP_005859.1 | |
| BET1 | NM_001317739.2 | c.235+114C>G | intron_variant | Intron 4 of 4 | NP_001304668.1 | |||
| BET1 | NR_133908.2 | n.374+114C>G | intron_variant | Intron 4 of 6 | ||||
| BET1 | NR_133909.2 | n.340+2027C>G | intron_variant | Intron 3 of 4 |
Ensembl
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152124
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452162Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 721414 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1452162
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
721414
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33016
American (AMR)
AF:
AC:
0
AN:
43286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25858
East Asian (EAS)
AF:
AC:
0
AN:
39550
South Asian (SAS)
AF:
AC:
0
AN:
83758
European-Finnish (FIN)
AF:
AC:
0
AN:
52928
Middle Eastern (MID)
AF:
AC:
0
AN:
5660
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1108070
Other (OTH)
AF:
AC:
0
AN:
60036
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74304 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152124
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74304
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41426
American (AMR)
AF:
AC:
0
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5198
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10610
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68004
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Mar 01, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
The c.349C>G (p.L117V) alteration is located in exon 4 (coding exon 4) of the BET1 gene. This alteration results from a C to G substitution at nucleotide position 349, causing the leucine (L) at amino acid position 117 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of MoRF binding (P = 0.1309);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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