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GeneBe

17-58309273-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_004758.4(TSPOAP1):c.3999G>A(p.Pro1333=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000499 in 1,613,936 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00051 ( 1 hom. )

Consequence

TSPOAP1
NM_004758.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.93
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 Likely_benign. Variant got -5 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-58309273-C-T is Benign according to our data. Variant chr17-58309273-C-T is described in ClinVar as [Benign]. Clinvar id is 732184.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-4.93 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSPOAP1NM_004758.4 linkuse as main transcriptc.3999G>A p.Pro1333= synonymous_variant 22/32 ENST00000343736.9
TSPOAP1NM_001261835.2 linkuse as main transcriptc.3999G>A p.Pro1333= synonymous_variant 22/32
TSPOAP1NM_024418.3 linkuse as main transcriptc.3819G>A p.Pro1273= synonymous_variant 21/31

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSPOAP1ENST00000343736.9 linkuse as main transcriptc.3999G>A p.Pro1333= synonymous_variant 22/321 NM_004758.4 P2O95153-1
TSPOAP1ENST00000268893.10 linkuse as main transcriptc.3819G>A p.Pro1273= synonymous_variant 21/311 A2O95153-2
TSPOAP1ENST00000580669.6 linkuse as main transcriptc.1395G>A p.Pro465= synonymous_variant 6/165
TSPOAP1ENST00000582679.1 linkuse as main transcriptc.421+694G>A intron_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000414
AC:
63
AN:
152174
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000523
Gnomad ASJ
AF:
0.00461
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000515
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000478
AC:
120
AN:
250890
Hom.:
1
AF XY:
0.000575
AC XY:
78
AN XY:
135646
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.000202
Gnomad ASJ exome
AF:
0.00596
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000424
Gnomad OTH exome
AF:
0.000652
GnomAD4 exome
AF:
0.000508
AC:
742
AN:
1461644
Hom.:
1
Cov.:
34
AF XY:
0.000476
AC XY:
346
AN XY:
727124
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.000201
Gnomad4 ASJ exome
AF:
0.00551
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.0000564
Gnomad4 NFE exome
AF:
0.000492
Gnomad4 OTH exome
AF:
0.000563
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000414
AC:
63
AN:
152292
Hom.:
0
Cov.:
33
AF XY:
0.000336
AC XY:
25
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.000523
Gnomad4 ASJ
AF:
0.00461
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000515
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000671
Hom.:
0
Bravo
AF:
0.000366
EpiCase
AF:
0.000382
EpiControl
AF:
0.000889

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
Cadd
Benign
0.028
Dann
Benign
0.47

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: rs141643991; hg19: chr17-56386634; API