rs35822882
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000339561.12(CLIC5):c.293C>A(p.Pro98His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 1,613,118 control chromosomes in the GnomAD database, including 589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 37 hom., cov: 32)
Exomes 𝑓: 0.024 ( 552 hom. )
Consequence
CLIC5
ENST00000339561.12 missense
ENST00000339561.12 missense
Scores
7
5
6
Clinical Significance
Conservation
PhyloP100: 9.97
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.006943047).
BP6
Variant 6-45949262-G-T is Benign according to our data. Variant chr6-45949262-G-T is described in ClinVar as [Benign]. Clinvar id is 508707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-45949262-G-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0171 (2597/152244) while in subpopulation NFE AF= 0.0274 (1864/68022). AF 95% confidence interval is 0.0264. There are 37 homozygotes in gnomad4. There are 1149 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 37 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC5 | NM_016929.5 | c.293C>A | p.Pro98His | missense_variant | 3/6 | ENST00000339561.12 | NP_058625.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC5 | ENST00000339561.12 | c.293C>A | p.Pro98His | missense_variant | 3/6 | 1 | NM_016929.5 | ENSP00000344165 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0171 AC: 2597AN: 152126Hom.: 37 Cov.: 32
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GnomAD3 exomes AF: 0.0165 AC: 4143AN: 251044Hom.: 55 AF XY: 0.0169 AC XY: 2290AN XY: 135632
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GnomAD4 exome AF: 0.0245 AC: 35791AN: 1460874Hom.: 552 Cov.: 30 AF XY: 0.0241 AC XY: 17496AN XY: 726698
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GnomAD4 genome AF: 0.0171 AC: 2597AN: 152244Hom.: 37 Cov.: 32 AF XY: 0.0154 AC XY: 1149AN XY: 74450
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TwinsUK
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131
ALSPAC
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101
ESP6500AA
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1948
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 14, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 25, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Pro257His in exon 3 of CLIC5: This variant is not expected to have clinical si gnificance because it has been identified in 2.46% (1639/66532) of European chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs35822882). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;.;T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;.;D;D;D
REVEL
Uncertain
Sift
Pathogenic
.;.;D;D;D
Sift4G
Pathogenic
.;.;D;D;D
Polyphen
1.0
.;.;D;.;.
Vest4
0.72, 0.71, 0.68
MPC
0.60
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at