21-34669629-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_053277.3(CLIC6):c.241G>A(p.Gly81Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000318 in 1,288,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_053277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC6 | NM_053277.3 | c.241G>A | p.Gly81Ser | missense_variant | 1/6 | ENST00000349499.3 | NP_444507.1 | |
CLIC6 | NM_001317009.2 | c.241G>A | p.Gly81Ser | missense_variant | 1/7 | NP_001303938.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC6 | ENST00000349499.3 | c.241G>A | p.Gly81Ser | missense_variant | 1/6 | 1 | NM_053277.3 | ENSP00000290332 | P2 | |
CLIC6 | ENST00000360731.7 | c.241G>A | p.Gly81Ser | missense_variant | 1/7 | 1 | ENSP00000353959 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152018Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000264 AC: 30AN: 1136230Hom.: 0 Cov.: 30 AF XY: 0.0000295 AC XY: 16AN XY: 542816
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2022 | The c.241G>A (p.G81S) alteration is located in exon 1 (coding exon 1) of the CLIC6 gene. This alteration results from a G to A substitution at nucleotide position 241, causing the glycine (G) at amino acid position 81 to be replaced by a serine (S). 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