rs368771637

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001128228.3(TPRN):​c.2073+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

TPRN
NM_001128228.3 intron

Scores

1
1
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47
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]

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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;
BP4
Computational evidence support a benign effect (MetaRNN=0.06939736).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TPRNNM_001128228.3 linkc.2073+10G>T intron_variant Intron 3 of 3 ENST00000409012.6 NP_001121700.2 Q4KMQ1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TPRNENST00000409012.6 linkc.2073+10G>T intron_variant Intron 3 of 3 1 NM_001128228.3 ENSP00000387100.4 Q4KMQ1-1
TPRNENST00000477345.1 linkn.2794+10G>T intron_variant Intron 2 of 2 1
TPRNENST00000333046.8 linkc.1477G>T p.Gly493Trp missense_variant Exon 3 of 3 2 ENSP00000327617.4 H3BLU1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
0.16
DANN
Benign
0.96
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.096
N
LIST_S2
Benign
0.28
T
M_CAP
Benign
0.0026
T
MetaRNN
Benign
0.069
T
MetaSVM
Benign
-0.97
T
PROVEAN
Benign
-0.30
N
REVEL
Benign
0.023
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.0050
D
MutPred
0.44
Loss of loop (P = 0.0128);
MVP
0.030
ClinPred
0.085
T
GERP RS
1.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs368771637; hg19: chr9-140086701; COSMIC: COSV58809242; COSMIC: COSV58809242; API