chr17-58306816-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004758.4(TSPOAP1):ā€‹c.5136T>Cā€‹(p.Ile1712=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00535 in 1,613,668 control chromosomes in the GnomAD database, including 415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.029 ( 207 hom., cov: 33)
Exomes š‘“: 0.0029 ( 208 hom. )

Consequence

TSPOAP1
NM_004758.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.919
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 -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 17-58306816-A-G is Benign according to our data. Variant chr17-58306816-A-G is described in ClinVar as [Benign]. Clinvar id is 789660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.919 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSPOAP1NM_004758.4 linkuse as main transcriptc.5136T>C p.Ile1712= synonymous_variant 25/32 ENST00000343736.9 NP_004749.2
TSPOAP1NM_001261835.2 linkuse as main transcriptc.5136T>C p.Ile1712= synonymous_variant 25/32 NP_001248764.1
TSPOAP1NM_024418.3 linkuse as main transcriptc.4956T>C p.Ile1652= synonymous_variant 24/31 NP_077729.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSPOAP1ENST00000343736.9 linkuse as main transcriptc.5136T>C p.Ile1712= synonymous_variant 25/321 NM_004758.4 ENSP00000345824 P2O95153-1

Frequencies

GnomAD3 genomes
AF:
0.0286
AC:
4354
AN:
152086
Hom.:
205
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.100
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0101
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.0182
GnomAD3 exomes
AF:
0.00723
AC:
1813
AN:
250600
Hom.:
79
AF XY:
0.00527
AC XY:
714
AN XY:
135554
show subpopulations
Gnomad AFR exome
AF:
0.0984
Gnomad AMR exome
AF:
0.00525
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000159
Gnomad OTH exome
AF:
0.00245
GnomAD4 exome
AF:
0.00292
AC:
4264
AN:
1461464
Hom.:
208
Cov.:
32
AF XY:
0.00245
AC XY:
1783
AN XY:
727032
show subpopulations
Gnomad4 AFR exome
AF:
0.104
Gnomad4 AMR exome
AF:
0.00597
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000336
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000630
Gnomad4 OTH exome
AF:
0.00667
GnomAD4 genome
AF:
0.0287
AC:
4368
AN:
152204
Hom.:
207
Cov.:
33
AF XY:
0.0274
AC XY:
2040
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.100
Gnomad4 AMR
AF:
0.0100
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.0180
Alfa
AF:
0.0124
Hom.:
45
Bravo
AF:
0.0324
Asia WGS
AF:
0.00693
AC:
24
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 26, 2017- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.65
DANN
Benign
0.59

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: rs111608552; hg19: chr17-56384177; API