chr2-55291767-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001365480.1(CCDC88A):c.5560A>G(p.Lys1854Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000866 in 1,611,482 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001365480.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5560A>G | p.Lys1854Glu | missense_variant | 32/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5557A>G | p.Lys1853Glu | missense_variant | 32/33 | ||
CCDC88A | NM_018084.5 | c.5476A>G | p.Lys1826Glu | missense_variant | 31/32 | ||
CCDC88A | NM_001254943.2 | c.5335A>G | p.Lys1779Glu | missense_variant | 33/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5560A>G | p.Lys1854Glu | missense_variant | 32/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.85+9333T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000762 AC: 116AN: 152186Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00153 AC: 382AN: 249776Hom.: 7 AF XY: 0.00135 AC XY: 182AN XY: 135120
GnomAD4 exome AF: 0.000877 AC: 1280AN: 1459178Hom.: 20 Cov.: 28 AF XY: 0.000913 AC XY: 663AN XY: 726036
GnomAD4 genome ? AF: 0.000762 AC: 116AN: 152304Hom.: 2 Cov.: 32 AF XY: 0.000913 AC XY: 68AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
CCDC88A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 13, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at