17-58308839-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004758.4(TSPOAP1):​c.4433G>A​(p.Arg1478His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )

Consequence

TSPOAP1
NM_004758.4 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0230
Variant links:
Genes affected
TSPOAP1 (HGNC:16831): (TSPO associated protein 1) Enables benzodiazepine receptor binding activity. Predicted to be involved in regulation of presynaptic cytosolic calcium ion concentration. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08754966).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSPOAP1NM_004758.4 linkuse as main transcriptc.4433G>A p.Arg1478His missense_variant 22/32 ENST00000343736.9 NP_004749.2
TSPOAP1NM_001261835.2 linkuse as main transcriptc.4433G>A p.Arg1478His missense_variant 22/32 NP_001248764.1
TSPOAP1NM_024418.3 linkuse as main transcriptc.4253G>A p.Arg1418His missense_variant 21/31 NP_077729.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSPOAP1ENST00000343736.9 linkuse as main transcriptc.4433G>A p.Arg1478His missense_variant 22/321 NM_004758.4 ENSP00000345824 P2O95153-1
TSPOAP1ENST00000268893.10 linkuse as main transcriptc.4253G>A p.Arg1418His missense_variant 21/311 ENSP00000268893 A2O95153-2
TSPOAP1ENST00000580669.6 linkuse as main transcriptc.1829G>A p.Arg610His missense_variant 6/165 ENSP00000462822
TSPOAP1ENST00000582679.1 linkuse as main transcriptc.422-898G>A intron_variant 5 ENSP00000462710

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152228
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000482
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000331
AC:
8
AN:
241518
Hom.:
0
AF XY:
0.0000226
AC XY:
3
AN XY:
132568
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000117
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000372
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000171
AC:
25
AN:
1458982
Hom.:
0
Cov.:
42
AF XY:
0.0000152
AC XY:
11
AN XY:
725642
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000153
Gnomad4 OTH exome
AF:
0.0000498
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152228
Hom.:
0
Cov.:
33
AF XY:
0.0000134
AC XY:
1
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0000482
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000192
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000452
Hom.:
0
Bravo
AF:
0.0000567
ExAC
AF:
0.00000829
AC:
1
EpiCase
AF:
0.000273
EpiControl
AF:
0.0000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 16, 2021The c.4433G>A (p.R1478H) alteration is located in exon 22 (coding exon 22) of the TSPOAP1 gene. This alteration results from a G to A substitution at nucleotide position 4433, causing the arginine (R) at amino acid position 1478 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.41
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
17
DANN
Uncertain
0.99
DEOGEN2
Benign
0.012
.;.;T
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.073
N
LIST_S2
Uncertain
0.86
D;D;D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.088
T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.3
.;.;L
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.79
N;.;N
REVEL
Benign
0.060
Sift
Benign
0.15
T;.;T
Sift4G
Benign
0.62
T;.;T
Polyphen
0.061
B;.;B
Vest4
0.17
MutPred
0.30
.;.;Loss of methylation at R1478 (P = 0.0126);
MVP
0.16
MPC
0.32
ClinPred
0.082
T
GERP RS
4.2
Varity_R
0.061
gMVP
0.52

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

LitVar

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

Other links and lift over

dbSNP: rs763316290; hg19: chr17-56386200; COSMIC: COSV99272378; COSMIC: COSV99272378; API