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GeneBe

17-58308856-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004758.4(TSPOAP1):c.4416T>C(p.Pro1472=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000434 in 1,609,020 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00024 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00045 ( 10 hom. )

Consequence

TSPOAP1
NM_004758.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.205
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 Benign. Variant got -11 ACMG points.

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=-0.86).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-58308856-A-G is Benign according to our data. Variant chr17-58308856-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2647959.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=0.205 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSPOAP1NM_004758.4 linkuse as main transcriptc.4416T>C p.Pro1472= synonymous_variant 22/32 ENST00000343736.9
TSPOAP1NM_001261835.2 linkuse as main transcriptc.4416T>C p.Pro1472= synonymous_variant 22/32
TSPOAP1NM_024418.3 linkuse as main transcriptc.4236T>C p.Pro1412= synonymous_variant 21/31

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSPOAP1ENST00000343736.9 linkuse as main transcriptc.4416T>C p.Pro1472= synonymous_variant 22/321 NM_004758.4 P2O95153-1
TSPOAP1ENST00000268893.10 linkuse as main transcriptc.4236T>C p.Pro1412= synonymous_variant 21/311 A2O95153-2
TSPOAP1ENST00000580669.6 linkuse as main transcriptc.1812T>C p.Pro604= synonymous_variant 6/165
TSPOAP1ENST00000582679.1 linkuse as main transcriptc.422-915T>C intron_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000237
AC:
36
AN:
152190
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00435
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000761
AC:
182
AN:
239236
Hom.:
4
AF XY:
0.00107
AC XY:
141
AN XY:
131430
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000587
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00521
Gnomad FIN exome
AF:
0.0000472
Gnomad NFE exome
AF:
0.000188
Gnomad OTH exome
AF:
0.000343
GnomAD4 exome
AF:
0.000454
AC:
662
AN:
1456712
Hom.:
10
Cov.:
40
AF XY:
0.000631
AC XY:
457
AN XY:
724218
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00566
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000113
Gnomad4 OTH exome
AF:
0.000548
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000236
AC:
36
AN:
152308
Hom.:
1
Cov.:
33
AF XY:
0.000322
AC XY:
24
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00435
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000214
Hom.:
0
Bravo
AF:
0.000227
Asia WGS
AF:
0.00202
AC:
7
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2022TSPOAP1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
3.5
Dann
Benign
0.60

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: rs527953790; hg19: chr17-56386217; API