chr12-48904424-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033124.5(CCDC65):c.88G>A(p.Glu30Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000539 in 1,614,102 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. E30D) has been classified as Uncertain significance.
Frequency
Consequence
NM_033124.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC65 | NM_033124.5 | c.88G>A | p.Glu30Lys | missense_variant | 1/8 | ENST00000320516.5 | |
CCDC65 | NM_001286957.2 | c.-302G>A | 5_prime_UTR_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC65 | ENST00000320516.5 | c.88G>A | p.Glu30Lys | missense_variant | 1/8 | 1 | NM_033124.5 | P2 | |
CCDC65 | ENST00000266984.9 | c.88G>A | p.Glu30Lys | missense_variant | 1/9 | 5 | A2 | ||
CCDC65 | ENST00000552942.5 | c.88G>A | p.Glu30Lys | missense_variant | 1/6 | 5 | |||
CCDC65 | ENST00000547861.5 | c.88G>A | p.Glu30Lys | missense_variant, NMD_transcript_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000104 AC: 26AN: 249078Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134830
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000756 AC XY: 55AN XY: 727212
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152282Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74462
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 27 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2022 | This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 30 of the CCDC65 protein (p.Glu30Lys). This variant is present in population databases (rs552481282, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with CCDC65-related conditions. 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at