rs727503521
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001128228.3(TPRN):c.1845_1847del(p.Glu621del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
TPRN
NM_001128228.3 inframe_deletion
NM_001128228.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.23
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 9-137192569-CTCT-C is Benign according to our data. Variant chr9-137192569-CTCT-C is described in ClinVar as [Benign]. Clinvar id is 165578.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-137192569-CTCT-C is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPRN | NM_001128228.3 | c.1845_1847del | p.Glu621del | inframe_deletion | 2/4 | ENST00000409012.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.1845_1847del | p.Glu621del | inframe_deletion | 2/4 | 1 | NM_001128228.3 | P1 | |
TPRN | ENST00000477345.1 | n.2566_2568del | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
TPRN | ENST00000333046.8 | c.1239_1241del | p.Glu419del | inframe_deletion | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 03, 2014 | Glu621del in exon 2 of TPRN: This variant is not expected to have clinical signi ficance because it has been identified in 5.7% (455/8007) of European American c hromosomes and 6.5% (268/4126) of African American chromosomes by the NHLBI Exom e Sequencing Project (http://evs.gs.washington.edu/EVS). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at