NM_001128228.3:c.2083G>A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001128228.3(TPRN):c.2083G>A(p.Ala695Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128228.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.2083G>A | p.Ala695Thr | missense_variant | Exon 4 of 4 | 1 | NM_001128228.3 | ENSP00000387100.4 | ||
TPRN | ENST00000477345.1 | n.2804G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
TPRN | ENST00000333046.8 | c.1561G>A | p.Ala521Thr | missense_variant | Exon 3 of 3 | 2 | ENSP00000327617.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250728Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135786
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461296Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726968
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Ala695Thr variant in TPRN has been previously reported in 1 family with no nsyndromic hearing loss who also carried a homozygous variant in another gene th at was a likely explanation for their hearing loss (Diaz-Horta 2012). The p.Ala6 95Thr variant is absent from large population studies. Computational prediction tools and conservation analysis suggest that this variant may impact the protein , though this information is not predictive enough to determine pathogenicity. I n summary, the clinical significance of the p.Ala695Thr variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at