rs267607135
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001128228.3(TPRN):c.1239G>A(p.Trp413Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000626 in 1,598,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001128228.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPRN | NM_001128228.3 | c.1239G>A | p.Trp413Ter | stop_gained | 1/4 | ENST00000409012.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.1239G>A | p.Trp413Ter | stop_gained | 1/4 | 1 | NM_001128228.3 | P1 | |
TPRN | ENST00000333046.8 | c.633G>A | p.Trp211Ter | stop_gained | 1/3 | 2 | |||
TPRN | ENST00000541945.1 | n.90+4631G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152264Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1446038Hom.: 0 Cov.: 34 AF XY: 0.00000696 AC XY: 5AN XY: 718258
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 79 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 12, 2010 | - - |
Hearing loss, autosomal recessive Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at