9-137192572-TTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001128228.3(TPRN):​c.1827_1844dupGGAGGAGGAGGAGGAGGA​(p.Glu610_Glu615dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,608,424 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

TPRN
NM_001128228.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 0.164
Variant links:
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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TPRNNM_001128228.3 linkc.1827_1844dupGGAGGAGGAGGAGGAGGA p.Glu610_Glu615dup disruptive_inframe_insertion 2/4 ENST00000409012.6 NP_001121700.2 Q4KMQ1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TPRNENST00000409012.6 linkc.1827_1844dupGGAGGAGGAGGAGGAGGA p.Glu610_Glu615dup disruptive_inframe_insertion 2/41 NM_001128228.3 ENSP00000387100.4 Q4KMQ1-1
TPRNENST00000477345.1 linkn.2548_2565dupGGAGGAGGAGGAGGAGGA non_coding_transcript_exon_variant 1/31
TPRNENST00000333046.8 linkc.1221_1238dupGGAGGAGGAGGAGGAGGA p.Glu408_Glu413dup disruptive_inframe_insertion 2/32 ENSP00000327617.4 H3BLU1

Frequencies

GnomAD3 genomes
AF:
0.0000595
AC:
9
AN:
151158
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000198
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.0000295
Gnomad OTH
AF:
0.000482
GnomAD4 exome
AF:
0.0000247
AC:
36
AN:
1457154
Hom.:
0
Cov.:
31
AF XY:
0.0000235
AC XY:
17
AN XY:
724714
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.0000902
Gnomad4 ASJ exome
AF:
0.0000768
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000135
Gnomad4 OTH exome
AF:
0.0000997
GnomAD4 genome
AF:
0.0000595
AC:
9
AN:
151270
Hom.:
0
Cov.:
33
AF XY:
0.0000541
AC XY:
4
AN XY:
73908
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000197
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000295
Gnomad4 OTH
AF:
0.000477

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJul 21, 2022This variant has not been reported in the literature in individuals affected with TPRN-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.1827_1844dup, results in the insertion of 6 amino acid(s) of the TPRN protein (p.Glu616_Glu621dup), but otherwise preserves the integrity of the reading frame. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
TPRN-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 19, 2023The TPRN c.1827_1844dup18 variant is predicted to result in an in-frame duplication (p.Glu616_Glu621dup). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs376810326; hg19: chr9-140087024; API