chr1-231547671-C-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005999.3(TSNAX):c.367+5060C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 150,978 control chromosomes in the GnomAD database, including 19,032 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.48 ( 19032 hom., cov: 30)
Consequence
TSNAX
NM_005999.3 intron
NM_005999.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.44
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSNAX | NM_005999.3 | c.367+5060C>A | intron_variant | ENST00000366639.9 | NP_005990.1 | |||
TSNAX-DISC1 | NR_028393.1 | n.525+5060C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSNAX | ENST00000366639.9 | c.367+5060C>A | intron_variant | 1 | NM_005999.3 | ENSP00000355599 | P1 | |||
TSNAX | ENST00000413309.3 | c.388+5060C>A | intron_variant | 3 | ENSP00000397537 | |||||
TSNAX | ENST00000475168.1 | n.3339+5060C>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
TSNAX | ENST00000602825.5 | n.511+5060C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.479 AC: 72247AN: 150858Hom.: 18974 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.479 AC: 72371AN: 150978Hom.: 19032 Cov.: 30 AF XY: 0.473 AC XY: 34867AN XY: 73722
GnomAD4 genome
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1732
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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