chr1-178514734-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032126.5(TEX35):c.125G>A(p.Arg42Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,840 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 (★).
Frequency
Consequence
NM_032126.5 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 | UniProt |
---|---|---|---|---|---|---|---|
TEX35 | NM_032126.5 | c.125G>A | p.Arg42Gln | missense_variant | 3/9 | ENST00000319416.7 | |
TEX35 | NM_001170722.2 | c.149G>A | p.Arg50Gln | missense_variant | 3/9 | ||
TEX35 | NM_001170723.2 | c.125G>A | p.Arg42Gln | missense_variant | 3/9 | ||
TEX35 | NM_001170724.2 | c.125G>A | p.Arg42Gln | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX35 | ENST00000319416.7 | c.125G>A | p.Arg42Gln | missense_variant | 3/9 | 1 | NM_032126.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250910Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135594
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461610Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727064
GnomAD4 genome AF: 0.000118 AC: 18AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.125G>A (p.R42Q) alteration is located in exon 3 (coding exon 3) of the TEX35 gene. This alteration results from a G to A substitution at nucleotide position 125, causing the arginine (R) at amino acid position 42 to be replaced by a glutamine (Q). 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