rs193920796
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000240361.12(TEX14):c.3281C>T(p.Ser1094Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,836 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 (no stars).
Frequency
Consequence
ENST00000240361.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX14 | NM_031272.5 | c.3172-1908C>T | intron_variant | ENST00000349033.10 | |||
TEX14 | NM_001201457.2 | c.3281C>T | p.Ser1094Leu | missense_variant | 20/33 | ||
TEX14 | NM_198393.4 | c.3263C>T | p.Ser1088Leu | missense_variant | 20/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX14 | ENST00000240361.12 | c.3281C>T | p.Ser1094Leu | missense_variant | 20/33 | 1 | A2 | ||
TEX14 | ENST00000389934.7 | c.3263C>T | p.Ser1088Leu | missense_variant | 20/33 | 1 | P4 | ||
TEX14 | ENST00000349033.10 | c.3172-1908C>T | intron_variant | 5 | NM_031272.5 | A2 | |||
TEX14 | ENST00000582740.1 | c.*3010-1908C>T | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251246Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135790
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461554Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727052
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74470
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at