rs371043030

Variant summary

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

The NM_001079512.4(TVP23A):ā€‹c.616G>Cā€‹(p.Glu206Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E206K) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.1e-7 ( 0 hom. )

Consequence

TVP23A
NM_001079512.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118
Variant links:
Genes affected
TVP23A (HGNC:20398): (trans-golgi network vesicle protein 23 homolog A) This gene encodes a membrane protein associated with the Golgi apparatus, which plays a crucial role in intracellular vesicular transport. The encoded protein is likely associated with the late (trans) Golgi compartments, which are involved in the delivery of secretory and membrane proteins to the endosome, lysosome or the plasma membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

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 (MetaRNN=0.015088052).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TVP23ANM_001079512.4 linkc.616G>C p.Glu206Gln missense_variant Exon 7 of 8 ENST00000299866.13 NP_001072980.1 A6NH52-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TVP23AENST00000299866.13 linkc.616G>C p.Glu206Gln missense_variant Exon 7 of 8 2 NM_001079512.4 ENSP00000299866.8 A6NH52-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000649
AC:
1
AN:
154174
Hom.:
0
AF XY:
0.0000122
AC XY:
1
AN XY:
81722
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000933
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
7.15e-7
AC:
1
AN:
1398712
Hom.:
0
Cov.:
31
AF XY:
0.00000145
AC XY:
1
AN XY:
689980
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000172
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000165
Hom.:
0
Bravo
AF:
0.00000378
ExAC
AF:
0.0000110
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
12
DANN
Benign
0.85
DEOGEN2
Benign
0.0094
T;.;T;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.064
N
LIST_S2
Benign
0.56
T;T;.;T
M_CAP
Benign
0.0059
T
MetaRNN
Benign
0.015
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N;.;N;.
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.33
.;.;N;.
REVEL
Benign
0.024
Sift
Benign
0.041
.;.;D;.
Sift4G
Benign
0.28
T;T;T;T
Polyphen
0.36
B;.;B;.
Vest4
0.17
MutPred
0.14
Gain of sheet (P = 0.0827);.;Gain of sheet (P = 0.0827);.;
MVP
0.014
MPC
0.050
ClinPred
0.022
T
GERP RS
0.17
Varity_R
0.071
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs371043030; hg19: chr16-10864155; API