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GeneBe

1-231529292-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.658 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSNAXNM_005999.3 linkuse as main transcriptc.54C>T p.Phe18= synonymous_variant 2/6 ENST00000366639.9
TSNAX-DISC1NR_028393.1 linkuse as main transcriptn.212C>T non_coding_transcript_exon_variant 2/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSNAXENST00000366639.9 linkuse as main transcriptc.54C>T p.Phe18= synonymous_variant 2/61 NM_005999.3 P1
TSNAXENST00000413309.3 linkuse as main transcriptc.54C>T p.Phe18= synonymous_variant 2/53
TSNAXENST00000476913.1 linkuse as main transcriptn.30C>T non_coding_transcript_exon_variant 1/33
TSNAXENST00000602825.5 linkuse as main transcriptn.198C>T non_coding_transcript_exon_variant 2/53

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00164
AC:
249
AN:
152148
Hom.:
0
Cov.:
33
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.:
1
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.:
7
Cov.:
31
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00164
AC:
250
AN:
152266
Hom.:
0
Cov.:
33
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.:
0
Bravo
AF:
0.00133
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.00224
EpiControl
AF:
0.00190

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 submitterclinical testingInvitaeApr 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
11
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.

Other links and lift over

dbSNP: rs138421350; hg19: chr1-231665038; API