chr2-55295598-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001365480.1(CCDC88A):c.5550T>C(p.Ser1850=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365480.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5550T>C | p.Ser1850= | splice_region_variant, synonymous_variant | 31/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5547T>C | p.Ser1849= | splice_region_variant, synonymous_variant | 31/33 | ||
CCDC88A | NM_018084.5 | c.5466T>C | p.Ser1822= | splice_region_variant, synonymous_variant | 30/32 | ||
CCDC88A | NM_001254943.2 | c.5325T>C | p.Ser1775= | splice_region_variant, synonymous_variant | 32/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5550T>C | p.Ser1850= | splice_region_variant, synonymous_variant | 31/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.85+13164A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251382Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135860
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461850Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727224
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 23, 2021 | 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 sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with CCDC88A-related conditions. This variant is present in population databases (rs760761141, ExAC 0.001%). This sequence change affects codon 1849 of the CCDC88A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the CCDC88A protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at