chr8-30836810-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PVS1_ModerateBP6BS2
The NM_001350162.2(TEX15):c.9474G>A(p.Trp3158*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000557 in 1,600,142 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001350162.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX15 | NM_001350162.2 | c.9474G>A | p.Trp3158* | stop_gained | Exon 10 of 11 | ENST00000643185.2 | NP_001337091.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX15 | ENST00000643185.2 | c.9474G>A | p.Trp3158* | stop_gained | Exon 10 of 11 | NM_001350162.2 | ENSP00000493555.1 | |||
TEX15 | ENST00000256246.5 | c.8325G>A | p.Trp2775* | stop_gained | Exon 3 of 4 | 1 | ENSP00000256246.2 | |||
TEX15 | ENST00000638951.1 | c.9486G>A | p.Trp3162* | stop_gained | Exon 9 of 10 | 5 | ENSP00000492713.1 |
Frequencies
GnomAD3 genomes AF: 0.000776 AC: 118AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000889 AC: 214AN: 240764Hom.: 0 AF XY: 0.000985 AC XY: 128AN XY: 129978
GnomAD4 exome AF: 0.000534 AC: 773AN: 1448178Hom.: 3 Cov.: 32 AF XY: 0.000552 AC XY: 397AN XY: 719428
GnomAD4 genome AF: 0.000776 AC: 118AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.00104 AC XY: 77AN XY: 74206
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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TEX15: PM2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at