Variant 17-58309361-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_004758.4(TSPOAP1):c.3911G>A(p.Cys1304Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00147 in 1,611,516 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0015 ( 3 hom. )

Consequence

TSPOAP1
NM_004758.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.82

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008192748).

BP6

Variant 17-58309361-C-T is Benign according to our data. Variant chr17-58309361-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 774522.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TSPOAP1	NM_004758.4 linkuse as main transcript	c.3911G>A	p.Cys1304Tyr	missense_variant	22/32	ENST00000343736.9
TSPOAP1	NM_001261835.2 linkuse as main transcript	c.3911G>A	p.Cys1304Tyr	missense_variant	22/32
TSPOAP1	NM_024418.3 linkuse as main transcript	c.3731G>A	p.Cys1244Tyr	missense_variant	21/31

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPOAP1	ENST00000343736.9 linkuse as main transcript	c.3911G>A	p.Cys1304Tyr	missense_variant	22/32	1	NM_004758.4	P2	O95153-1
TSPOAP1	ENST00000268893.10 linkuse as main transcript	c.3731G>A	p.Cys1244Tyr	missense_variant	21/31	1		A2	O95153-2
TSPOAP1	ENST00000580669.6 linkuse as main transcript	c.1307G>A	p.Cys436Tyr	missense_variant	6/16	5
TSPOAP1	ENST00000582679.1 linkuse as main transcript	c.421+606G>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00131

AC:

199

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00226

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.000958

AC:

234

AN:

244318

Hom.:

AF XY:

0.000972

AC XY:

129

AN XY:

132758

show subpopulations

Gnomad AFR exome

AF:

0.000314

Gnomad AMR exome

AF:

0.000522

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000230

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00183

Gnomad OTH exome

AF:

0.000662

GnomAD4 exome

AF:

0.00149

AC:

2176

AN:

1459268

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

1062

AN XY:

725874

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000649

Gnomad4 ASJ exome

AF:

0.0000767

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000220

Gnomad4 FIN exome

AF:

0.0000387

Gnomad4 NFE exome

AF:

0.00181

Gnomad4 OTH exome

AF:

0.00119

GnomAD4 genome

AF:

0.00131

AC:

199

AN:

152248

Hom.:

Cov.:

AF XY:

0.00118

AC XY:

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.000337

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00226

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00167

Hom.:

Bravo

AF:

0.00125

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00174

AC:

ExAC

AF:

0.00103

AC:

125

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00191

EpiControl

AF:

0.00267

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 submitter

clinical testing

Invitae

Jul 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.13

Cadd

Benign

Dann

Benign

0.94

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.11

FATHMM_MKL

Uncertain

0.86

LIST_S2

Uncertain

0.87

D;D;D

M_CAP

Uncertain

0.24

MetaRNN

Benign

0.0082

T;T;T

MetaSVM

Benign

-0.35

MutationTaster

Benign

0.86

N;N;N

PrimateAI

Uncertain

0.59

PROVEAN

Pathogenic

-4.5

D;.;D

REVEL

Uncertain

0.34

Sift

Uncertain

0.0040

D;.;D

Sift4G

Uncertain

0.057

T;.;T

Polyphen

0.63

P;.;B

Vest4

0.52

MVP

0.73

MPC

0.57

ClinPred

0.079

GERP RS

3.4

Varity_R

0.46

gMVP

0.35

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.

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