ENST00000185206.12:c.237A>T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000185206.12(CLIC5):c.237A>T(p.Arg79Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00359 in 1,551,702 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000185206.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC5 | NM_001114086.2 | c.237A>T | p.Arg79Ser | missense_variant | Exon 1 of 6 | NP_001107558.1 | ||
CLIC5 | NM_001370650.1 | c.237A>T | p.Arg79Ser | missense_variant | Exon 2 of 7 | NP_001357579.1 | ||
CLIC5 | XM_011514692.4 | c.237A>T | p.Arg79Ser | missense_variant | Exon 1 of 7 | XP_011512994.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00303 AC: 461AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00273 AC: 427AN: 156382Hom.: 3 AF XY: 0.00276 AC XY: 229AN XY: 82882
GnomAD4 exome AF: 0.00366 AC: 5115AN: 1399394Hom.: 16 Cov.: 34 AF XY: 0.00364 AC XY: 2512AN XY: 690206
GnomAD4 genome AF: 0.00303 AC: 461AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.00279 AC XY: 208AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:4
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CLIC5: BP4, BS2 -
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not specified Benign:1
p.Arg79Ser in exon 1 of CLIC5: This variant is not expected to have clinical sig nificance because it has been identified in 0.52% (46/8766) of European chromoso mes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; d bSNP rs41271277). -
Autosomal recessive nonsyndromic hearing loss 103 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at