1-46673022-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The ENST00000415500.1(TEX38):c.-40-2A>T variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000844 in 1,551,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000415500.1 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX38 | NM_001145474.4 | c.187A>T | p.Ser63Cys | missense_variant | 2/2 | ENST00000334122.5 | |
TEX38 | NM_001300864.2 | c.-40-2A>T | splice_acceptor_variant | ||||
TEX38 | NM_001300863.2 | c.25A>T | p.Ser9Cys | missense_variant | 2/2 | ||
TEX38 | XM_011541421.4 | c.190A>T | p.Ser64Cys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX38 | ENST00000334122.5 | c.187A>T | p.Ser63Cys | missense_variant | 2/2 | 1 | NM_001145474.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000243 AC: 38AN: 156154Hom.: 0 AF XY: 0.000290 AC XY: 24AN XY: 82764
GnomAD4 exome AF: 0.0000879 AC: 123AN: 1399400Hom.: 0 Cov.: 31 AF XY: 0.000112 AC XY: 77AN XY: 690212
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.187A>T (p.S63C) alteration is located in exon 2 (coding exon 2) of the TEX38 gene. This alteration results from a A to T substitution at nucleotide position 187, causing the serine (S) at amino acid position 63 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at