6-46079903-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001114086.2(CLIC5):āc.340A>Gā(p.Thr114Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 1,551,914 control chromosomes in the GnomAD database, including 1,820 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001114086.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC5 | NM_001114086.2 | c.340A>G | p.Thr114Ala | missense_variant | 1/6 | NP_001107558.1 | ||
CLIC5 | NM_001370650.1 | c.340A>G | p.Thr114Ala | missense_variant | 2/7 | NP_001357579.1 | ||
CLIC5 | XM_011514692.4 | c.340A>G | p.Thr114Ala | missense_variant | 1/7 | XP_011512994.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC5 | ENST00000185206.12 | c.340A>G | p.Thr114Ala | missense_variant | 1/6 | 1 | ENSP00000185206.6 |
Frequencies
GnomAD3 genomes AF: 0.0459 AC: 6979AN: 152124Hom.: 160 Cov.: 32
GnomAD3 exomes AF: 0.0433 AC: 6830AN: 157570Hom.: 184 AF XY: 0.0426 AC XY: 3540AN XY: 83124
GnomAD4 exome AF: 0.0471 AC: 65897AN: 1399672Hom.: 1659 Cov.: 34 AF XY: 0.0467 AC XY: 32251AN XY: 690336
GnomAD4 genome AF: 0.0459 AC: 6993AN: 152242Hom.: 161 Cov.: 32 AF XY: 0.0458 AC XY: 3406AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Thr114Ala in exon 1 of CLIC5: This variant is not expected to have clinical si gnificance because it has been identified in 7.59% (126/1660) of Finnish chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs723580). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at