Variant 1-231529292-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_005999.3(TSNAX):c.54C>T(p.Phe18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0022 in 1,614,122 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0023 ( 7 hom. )

Consequence

TSNAX
NM_005999.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.658

Variant links:

Genes affected

TSNAX (HGNC:12380): (translin associated factor X) This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs. [provided by RefSeq, Jul 2008]

TSNAX links:

TSNAX-DISC1 (HGNC:):

TSNAX-DISC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 1-231529292-C-T is Benign according to our data. Variant chr1-231529292-C-T is described in ClinVar as [Benign]. Clinvar id is 784454.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.658 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSNAX	NM_005999.3 linkuse as main transcript	c.54C>T	p.Phe18=	synonymous_variant	2/6	ENST00000366639.9	NP_005990.1
TSNAX-DISC1	NR_028393.1 linkuse as main transcript	n.212C>T		non_coding_transcript_exon_variant	2/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TSNAX	ENST00000366639.9 linkuse as main transcript	c.54C>T	p.Phe18=	synonymous_variant	2/6	1	NM_005999.3	ENSP00000355599	P1
TSNAX	ENST00000413309.3 linkuse as main transcript	c.54C>T	p.Phe18=	synonymous_variant	2/5	3		ENSP00000397537
TSNAX	ENST00000476913.1 linkuse as main transcript	n.30C>T		non_coding_transcript_exon_variant	1/3	3
TSNAX	ENST00000602825.5 linkuse as main transcript	n.198C>T		non_coding_transcript_exon_variant	2/5	3

Frequencies

GnomAD3 genomes

AF:

0.00164

AC:

249

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000290

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.00367

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00232

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00193

AC:

479

AN:

248728

Hom.:

AF XY:

0.00216

AC XY:

291

AN XY:

134704

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00373

Gnomad FIN exome

AF:

0.00296

Gnomad NFE exome

AF:

0.00213

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00225

AC:

3293

AN:

1461856

Hom.:

Cov.:

AF XY:

0.00229

AC XY:

1666

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.00145

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00379

Gnomad4 FIN exome

AF:

0.00290

Gnomad4 NFE exome

AF:

0.00235

Gnomad4 OTH exome

AF:

0.00197

GnomAD4 genome

AF:

0.00164

AC:

250

AN:

152266

Hom.:

Cov.:

AF XY:

0.00167

AC XY:

124

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.00367

Gnomad4 NFE

AF:

0.00232

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00195

Hom.:

Bravo

AF:

0.00133

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00224

EpiControl

AF:

0.00190

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	Labcorp Genetics (formerly Invitae), Labcorp	Apr 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Benign

0.82

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