1-231529288-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005999.3(TSNAX):c.50A>G(p.Asn17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00363 in 1,614,138 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0036 ( 14 hom. )
Consequence
TSNAX
NM_005999.3 missense
NM_005999.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 2.81
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004289776).
BP6
?
Variant 1-231529288-A-G is Benign according to our data. Variant chr1-231529288-A-G is described in ClinVar as [Benign]. Clinvar id is 718408.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSNAX | NM_005999.3 | c.50A>G | p.Asn17Ser | missense_variant | 2/6 | ENST00000366639.9 | |
TSNAX-DISC1 | NR_028393.1 | n.208A>G | non_coding_transcript_exon_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSNAX | ENST00000366639.9 | c.50A>G | p.Asn17Ser | missense_variant | 2/6 | 1 | NM_005999.3 | P1 | |
TSNAX | ENST00000413309.3 | c.50A>G | p.Asn17Ser | missense_variant | 2/5 | 3 | |||
TSNAX | ENST00000476913.1 | n.26A>G | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
TSNAX | ENST00000602825.5 | n.194A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00344 AC: 523AN: 152196Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00343 AC: 853AN: 248690Hom.: 4 AF XY: 0.00353 AC XY: 476AN XY: 134698
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GnomAD4 exome AF: 0.00365 AC: 5335AN: 1461826Hom.: 14 Cov.: 31 AF XY: 0.00365 AC XY: 2652AN XY: 727218
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ESP6500AA
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ExAC
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423
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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 | Mar 31, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at