Variant 17-58310741-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004758.4(TSPOAP1):c.3470G>T(p.Gly1157Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0053 in 1,612,064 control chromosomes in the GnomAD database, including 407 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 204 hom., cov: 33)

Exomes 𝑓: 0.0029 ( 203 hom. )

Consequence

TSPOAP1
NM_004758.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.858

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]

TSPOAP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019123852).

BP6

Variant 17-58310741-C-A is Benign according to our data. Variant chr17-58310741-C-A is described in ClinVar as [Benign]. Clinvar id is 781373.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TSPOAP1	NM_004758.4 linkuse as main transcript	c.3470G>T	p.Gly1157Val	missense_variant	20/32	ENST00000343736.9
TSPOAP1	NM_001261835.2 linkuse as main transcript	c.3470G>T	p.Gly1157Val	missense_variant	20/32
TSPOAP1	NM_024418.3 linkuse as main transcript	c.3290G>T	p.Gly1097Val	missense_variant	19/31

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPOAP1	ENST00000343736.9 linkuse as main transcript	c.3470G>T	p.Gly1157Val	missense_variant	20/32	1	NM_004758.4	P2	O95153-1
TSPOAP1	ENST00000268893.10 linkuse as main transcript	c.3290G>T	p.Gly1097Val	missense_variant	19/31	1		A2	O95153-2
TSPOAP1	ENST00000580669.6 linkuse as main transcript	c.866G>T	p.Gly289Val	missense_variant	4/16	5
TSPOAP1	ENST00000582679.1 linkuse as main transcript			upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0285

AC:

4336

AN:

152174

Hom.:

202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0997

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00962

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:

0.000221

Gnomad OTH

AF:

0.0181

GnomAD3 exomes

AF:

0.00697

AC:

1714

AN:

245838

Hom.:

AF XY:

0.00512

AC XY:

686

AN XY:

133916

show subpopulations

Gnomad AFR exome

AF:

0.0981

Gnomad AMR exome

AF:

0.00490

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000197

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000155

Gnomad OTH exome

AF:

0.00215

GnomAD4 exome

AF:

0.00287

AC:

4196

AN:

1459772

Hom.:

203

Cov.:

AF XY:

0.00241

AC XY:

1748

AN XY:

726028

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.00555

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:

0.0000603

Gnomad4 OTH exome

AF:

0.00655

GnomAD4 genome

AF:

0.0286

AC:

4350

AN:

152292

Hom.:

204

Cov.:

AF XY:

0.0271

AC XY:

2019

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0998

Gnomad4 AMR

AF:

0.00954

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.00892

Hom.:

Bravo

AF:

0.0322

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0806

AC:

354

ESP6500EA

AF:

0.000117

AC:

ExAC

AF:

0.00863

AC:

1046

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000237

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 submitter

clinical testing

Invitae

Feb 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.57

Cadd

Benign

Dann

Benign

0.87

Eigen

Benign

-0.53

Eigen_PC

Benign

-0.56

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.72

T;T;T

MetaRNN

Benign

0.0019

T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.98

N;N;N

PrimateAI

Benign

0.30

PROVEAN

Benign

-2.2

N;.;N

REVEL

Benign

0.058

Sift

Uncertain

0.0090

D;.;D

Sift4G

Benign

0.27

T;.;T

Polyphen

0.74

P;.;B

Vest4

0.28

MVP

0.16

MPC

0.26

ClinPred

0.018

GERP RS

4.6

Varity_R

0.21

gMVP

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over