8-81758142-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_152284.4(CHMP4C):c.484G>A(p.Asp162Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152284.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHMP4C | NM_152284.4 | c.484G>A | p.Asp162Asn | missense_variant, splice_region_variant | 4/5 | ENST00000297265.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHMP4C | ENST00000297265.5 | c.484G>A | p.Asp162Asn | missense_variant, splice_region_variant | 4/5 | 1 | NM_152284.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250910Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135606
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461514Hom.: 0 Cov.: 31 AF XY: 0.0000922 AC XY: 67AN XY: 727066
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.484G>A (p.D162N) alteration is located in exon 4 (coding exon 4) of the CHMP4C gene. This alteration results from a G to A substitution at nucleotide position 484, causing the aspartic acid (D) at amino acid position 162 to be replaced by an asparagine (N). 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