chr19-32879206-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032816.5(CEP89):c.2308G>A(p.Asp770Asn) 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 1,461,708 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 (★). Synonymous variant affecting the same amino acid position (i.e. D770D) has been classified as Likely benign.
Frequency
Consequence
NM_032816.5 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 |
---|---|---|---|---|---|---|---|
CEP89 | NM_032816.5 | c.2308G>A | p.Asp770Asn | missense_variant | 19/19 | ENST00000305768.10 | |
CEP89 | XM_005259344.4 | c.2236G>A | p.Asp746Asn | missense_variant | 19/19 | ||
CEP89 | XM_047439562.1 | c.1567G>A | p.Asp523Asn | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP89 | ENST00000305768.10 | c.2308G>A | p.Asp770Asn | missense_variant | 19/19 | 1 | NM_032816.5 | P3 | |
CEP89 | ENST00000586984.6 | c.*917G>A | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 1 | ||||
CEP89 | ENST00000591698.5 | c.*1642G>A | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152194Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251148Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135734
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461708Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727130
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.2308G>A (p.D770N) alteration is located in exon 19 (coding exon 19) of the CEP89 gene. This alteration results from a G to A substitution at nucleotide position 2308, causing the aspartic acid (D) at amino acid position 770 to be replaced by an asparagine (N). 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