X-155279971-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001289.6(CLIC2):c.391G>A(p.Ala131Thr) variant causes a missense 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. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001289.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC2 | ENST00000369449.7 | c.391G>A | p.Ala131Thr | missense_variant | 4/6 | 1 | NM_001289.6 | ENSP00000358460.2 | ||
CLIC2 | ENST00000321926.4 | c.265G>A | p.Ala89Thr | missense_variant | 3/4 | 3 | ENSP00000318558.4 | |||
CLIC2 | ENST00000465553.5 | n.506G>A | non_coding_transcript_exon_variant | 4/7 | 3 | |||||
CLIC2 | ENST00000491205.1 | n.445G>A | non_coding_transcript_exon_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1067054Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 337530
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 10, 2024 | The c.391G>A (p.A131T) alteration is located in exon 4 (coding exon 4) of the CLIC2 gene. This alteration results from a G to A substitution at nucleotide position 391, causing the alanine (A) at amino acid position 131 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.