chr2-55295651-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_001365480.1(CCDC88A):āc.5497A>Gā(p.Ile1833Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1833L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365480.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5497A>G | p.Ile1833Val | missense_variant | 31/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5494A>G | p.Ile1832Val | missense_variant | 31/33 | ||
CCDC88A | NM_018084.5 | c.5413A>G | p.Ile1805Val | missense_variant | 30/32 | ||
CCDC88A | NM_001254943.2 | c.5272A>G | p.Ile1758Val | missense_variant | 32/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5497A>G | p.Ile1833Val | missense_variant | 31/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.86-13181T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251474Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135908
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000426 AC XY: 31AN XY: 727248
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74370
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1377987). This variant has not been reported in the literature in individuals affected with CCDC88A-related conditions. This variant is present in population databases (rs367582957, gnomAD 0.03%). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1832 of the CCDC88A protein (p.Ile1832Val). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at