chr1-229326945-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145257.5(CCSAP):c.429C>A(p.Asp143Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,878 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 (★).
Frequency
Consequence
NM_145257.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCSAP | NM_145257.5 | c.429C>A | p.Asp143Glu | missense_variant | 3/4 | ENST00000284617.7 | |
CCSAP | NM_001410936.1 | c.87C>A | p.Asp29Glu | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCSAP | ENST00000284617.7 | c.429C>A | p.Asp143Glu | missense_variant | 3/4 | 1 | NM_145257.5 | P1 | |
CCSAP | ENST00000366687.5 | c.429C>A | p.Asp143Glu | missense_variant | 2/3 | 1 | P1 | ||
CCSAP | ENST00000483092.1 | n.1412C>A | non_coding_transcript_exon_variant | 3/4 | 1 | ||||
CCSAP | ENST00000366686.1 | c.87C>A | p.Asp29Glu | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.429C>A (p.D143E) alteration is located in exon 3 (coding exon 2) of the CCSAP gene. This alteration results from a C to A substitution at nucleotide position 429, causing the aspartic acid (D) at amino acid position 143 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.