17-58559452-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_031272.5(TEX14):c.4267+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,281,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_031272.5 splice_donor, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX14 | NM_031272.5 | c.4267+1G>A | splice_donor_variant, intron_variant | Intron 30 of 31 | ENST00000349033.10 | NP_112562.3 | ||
TEX14 | NM_001201457.2 | c.4405+1G>A | splice_donor_variant, intron_variant | Intron 31 of 32 | NP_001188386.1 | |||
TEX14 | NM_198393.4 | c.4387+1G>A | splice_donor_variant, intron_variant | Intron 31 of 32 | NP_938207.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000367 AC: 9AN: 245090Hom.: 0 AF XY: 0.0000679 AC XY: 9AN XY: 132470
GnomAD4 exome AF: 0.0000292 AC: 33AN: 1129708Hom.: 0 Cov.: 16 AF XY: 0.0000485 AC XY: 28AN XY: 577270
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74478
ClinVar
Submissions by phenotype
Male infertility with azoospermia or oligozoospermia due to single gene mutation Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at