chrX-155299128-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001289.6(CLIC2):āc.75G>Cā(p.Glu25Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,198,587 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001289.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC2 | NM_001289.6 | c.75G>C | p.Glu25Asp | missense_variant | 2/6 | ENST00000369449.7 | NP_001280.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC2 | ENST00000369449.7 | c.75G>C | p.Glu25Asp | missense_variant | 2/6 | 1 | NM_001289.6 | ENSP00000358460.2 | ||
CLIC2 | ENST00000321926.4 | c.75G>C | p.Glu25Asp | missense_variant | 2/4 | 3 | ENSP00000318558.4 | |||
CLIC2 | ENST00000465553.5 | n.190G>C | non_coding_transcript_exon_variant | 2/7 | 3 | |||||
CLIC2 | ENST00000491205.1 | n.129G>C | non_coding_transcript_exon_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111471Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33667
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182932Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67448
GnomAD4 exome AF: 0.00000184 AC: 2AN: 1087116Hom.: 0 Cov.: 28 AF XY: 0.00000283 AC XY: 1AN XY: 352908
GnomAD4 genome AF: 0.00000897 AC: 1AN: 111471Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33667
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.75G>C (p.E25D) alteration is located in exon 2 (coding exon 2) of the CLIC2 gene. This alteration results from a G to C substitution at nucleotide position 75, causing the glutamic acid (E) at amino acid position 25 to be replaced by an aspartic acid (D). 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