chr13-30956954-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152325.3(TEX26):āc.394A>Gā(p.Met132Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,236 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152325.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX26 | NM_152325.3 | c.394A>G | p.Met132Val | missense_variant | 4/7 | ENST00000380473.8 | NP_689538.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX26 | ENST00000380473.8 | c.394A>G | p.Met132Val | missense_variant | 4/7 | 1 | NM_152325.3 | ENSP00000369840 | P1 | |
TEX26 | ENST00000531960.1 | c.*33A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 3 | ENSP00000435263 | ||||
TEX26 | ENST00000530916.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251462Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135904
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461862Hom.: 0 Cov.: 34 AF XY: 0.0000770 AC XY: 56AN XY: 727240
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.394A>G (p.M132V) alteration is located in exon 4 (coding exon 4) of the TEX26 gene. This alteration results from a A to G substitution at nucleotide position 394, causing the methionine (M) at amino acid position 132 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