13-111328285-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000283547.2(TEX29):c.161C>T(p.Ala54Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,613,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000283547.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX29 | NM_152324.3 | c.161C>T | p.Ala54Val | missense_variant | 3/6 | ENST00000283547.2 | NP_689537.1 | |
TEX29 | NM_001303133.1 | c.85C>T | p.Arg29Trp | missense_variant | 3/7 | NP_001290062.1 | ||
TEX29 | XM_017020387.2 | c.242C>T | p.Ala81Val | missense_variant | 3/6 | XP_016875876.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX29 | ENST00000283547.2 | c.161C>T | p.Ala54Val | missense_variant | 3/6 | 1 | NM_152324.3 | ENSP00000283547 | P1 | |
TEX29 | ENST00000497241.5 | c.242C>T | p.Ala81Val | missense_variant, NMD_transcript_variant | 3/7 | 5 | ENSP00000431661 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251352Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135858
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1460688Hom.: 0 Cov.: 32 AF XY: 0.0000757 AC XY: 55AN XY: 726686
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.161C>T (p.A54V) alteration is located in exon 3 (coding exon 2) of the TEX29 gene. This alteration results from a C to T substitution at nucleotide position 161, causing the alanine (A) at amino acid position 54 to be replaced by a valine (V). 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