Variant chr17-58308997-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004758.4(TSPOAP1):c.4275A>T(p.Arg1425=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,612,302 control chromosomes in the GnomAD database, including 70,073 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6642 hom., cov: 33)

Exomes 𝑓: 0.29 ( 63431 hom. )

Consequence

TSPOAP1
NM_004758.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.03

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 17-58308997-T-A is Benign according to our data. Variant chr17-58308997-T-A is described in ClinVar as [Benign]. Clinvar id is 1294164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TSPOAP1	NM_004758.4 linkuse as main transcript	c.4275A>T	p.Arg1425=	synonymous_variant	22/32	ENST00000343736.9
TSPOAP1	NM_001261835.2 linkuse as main transcript	c.4275A>T	p.Arg1425=	synonymous_variant	22/32
TSPOAP1	NM_024418.3 linkuse as main transcript	c.4095A>T	p.Arg1365=	synonymous_variant	21/31

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPOAP1	ENST00000343736.9 linkuse as main transcript	c.4275A>T	p.Arg1425=	synonymous_variant	22/32	1	NM_004758.4	P2	O95153-1
TSPOAP1	ENST00000268893.10 linkuse as main transcript	c.4095A>T	p.Arg1365=	synonymous_variant	21/31	1		A2	O95153-2
TSPOAP1	ENST00000580669.6 linkuse as main transcript	c.1671A>T	p.Arg557=	synonymous_variant	6/16	5
TSPOAP1	ENST00000582679.1 linkuse as main transcript	c.421+970A>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44850

AN:

152032

Hom.:

6630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.320

GnomAD3 exomes

AF:

0.282

AC:

69485

AN:

246376

Hom.:

10058

AF XY:

0.283

AC XY:

37946

AN XY:

134270

show subpopulations

Gnomad AFR exome

AF:

0.294

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.319

Gnomad EAS exome

AF:

0.234

Gnomad SAS exome

AF:

0.249

Gnomad FIN exome

AF:

0.319

Gnomad NFE exome

AF:

0.304

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.293

AC:

427995

AN:

1460152

Hom.:

63431

Cov.:

AF XY:

0.291

AC XY:

211713

AN XY:

726396

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.231

Gnomad4 ASJ exome

AF:

0.320

Gnomad4 EAS exome

AF:

0.224

Gnomad4 SAS exome

AF:

0.245

Gnomad4 FIN exome

AF:

0.324

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.290

GnomAD4 genome

AF:

0.295

AC:

44886

AN:

152150

Hom.:

6642

Cov.:

AF XY:

0.294

AC XY:

21894

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.292

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.301

Hom.:

2264

Bravo

AF:

0.292

Asia WGS

AF:

0.219

AC:

763

AN:

3478

EpiCase

AF:

0.301

EpiControl

AF:

0.309

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 submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 26, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.20

DANN

Benign

0.65

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