rs28417902
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001128228.3(TPRN):c.1726-1487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,378 control chromosomes in the GnomAD database, including 2,038 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.097 ( 2038 hom., cov: 33)
Exomes 𝑓: 0.024 ( 0 hom. )
Consequence
TPRN
NM_001128228.3 intron
NM_001128228.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.51
Genes affected
TPRN (HGNC:26894): (taperin) This locus encodes a sensory epithelial protein. It was defined by linkage analysis in three Pakistani families to lie between D9S1818 (centromeric) and D9SH6 (telomeric). Mutations at this locus have been associated with autosomal recessive deafness. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPRN | NM_001128228.3 | c.1726-1487C>T | intron_variant | ENST00000409012.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.1726-1487C>T | intron_variant | 1 | NM_001128228.3 | P1 | |||
TPRN | ENST00000477345.1 | n.960C>T | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
TPRN | ENST00000333046.8 | c.1120-1487C>T | intron_variant | 2 | |||||
TPRN | ENST00000541945.1 | n.91-1487C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0972 AC: 14780AN: 152094Hom.: 2036 Cov.: 33
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GnomAD4 exome AF: 0.0241 AC: 4AN: 166Hom.: 0 Cov.: 0 AF XY: 0.0161 AC XY: 2AN XY: 124
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GnomAD4 genome ? AF: 0.0973 AC: 14808AN: 152212Hom.: 2038 Cov.: 33 AF XY: 0.0969 AC XY: 7211AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at