NM_016929.5:c.407-5927T>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016929.5(CLIC5):c.407-5927T>A 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: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CLIC5
NM_016929.5 intron
NM_016929.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.340
Publications
7 publications found
Genes affected
CLIC5 (HGNC:13517): (chloride intracellular channel 5) This gene encodes a member of the chloride intracellular channel (CLIC) family of chloride ion channels. The encoded protein associates with actin-based cytoskeletal structures and may play a role in multiple processes including hair cell stereocilia formation, myoblast proliferation and glomerular podocyte and endothelial cell maintenance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
CLIC5 Gene-Disease associations (from GenCC):
- autosomal recessive nonsyndromic hearing loss 103Inheritance: Unknown, AR Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
- hearing loss, autosomal recessiveInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 812092Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 375548
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
812092
Hom.:
Cov.:
15
AF XY:
AC XY:
0
AN XY:
375548
African (AFR)
AF:
AC:
0
AN:
15488
American (AMR)
AF:
AC:
0
AN:
964
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5024
East Asian (EAS)
AF:
AC:
0
AN:
3504
South Asian (SAS)
AF:
AC:
0
AN:
15968
European-Finnish (FIN)
AF:
AC:
0
AN:
264
Middle Eastern (MID)
AF:
AC:
0
AN:
1586
European-Non Finnish (NFE)
AF:
AC:
0
AN:
742710
Other (OTH)
AF:
AC:
0
AN:
26584
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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