chr2-55291745-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001365480.1(CCDC88A):c.5582C>T(p.Ser1861Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,459,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1861A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365480.1 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 | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5582C>T | p.Ser1861Leu | missense_variant | 32/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5579C>T | p.Ser1860Leu | missense_variant | 32/33 | ||
CCDC88A | NM_018084.5 | c.5498C>T | p.Ser1833Leu | missense_variant | 31/32 | ||
CCDC88A | NM_001254943.2 | c.5357C>T | p.Ser1786Leu | missense_variant | 33/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5582C>T | p.Ser1861Leu | missense_variant | 32/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.85+9311G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250094Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135274
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1459966Hom.: 0 Cov.: 28 AF XY: 0.00000826 AC XY: 6AN XY: 726370
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 04, 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with CCDC88A-related conditions. This variant is present in population databases (rs762237924, gnomAD 0.0009%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1860 of the CCDC88A protein (p.Ser1860Leu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at