9-137192307-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001128228.3(TPRN):c.2025G>A(p.Ala675=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,460,650 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
TPRN
NM_001128228.3 synonymous
NM_001128228.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.09
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 9-137192307-C-T is Benign according to our data. Variant chr9-137192307-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1903706.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.09 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| TPRN | NM_001128228.3 | c.2025G>A | p.Ala675= | synonymous_variant | 3/4 | ENST00000409012.6 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TPRN | ENST00000409012.6 | c.2025G>A | p.Ala675= | synonymous_variant | 3/4 | 1 | NM_001128228.3 | P1 | |
| TPRN | ENST00000477345.1 | n.2746G>A | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
| TPRN | ENST00000333046.8 | c.1419G>A | p.Ala473= | synonymous_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248682Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135182
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GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460650Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726642
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GnomAD4 genome
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33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at