chr2-65072318-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015147.3(CEP68):c.1222G>A(p.Asp408Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000328 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015147.3 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 |
---|---|---|---|---|---|---|---|
CEP68 | NM_015147.3 | c.1222G>A | p.Asp408Asn | missense_variant | 3/7 | ENST00000377990.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP68 | ENST00000377990.7 | c.1222G>A | p.Asp408Asn | missense_variant | 3/7 | 1 | NM_015147.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251144Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135778
GnomAD4 exome AF: 0.000345 AC: 505AN: 1461790Hom.: 0 Cov.: 33 AF XY: 0.000341 AC XY: 248AN XY: 727198
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.1222G>A (p.D408N) alteration is located in exon 3 (coding exon 2) of the CEP68 gene. This alteration results from a G to A substitution at nucleotide position 1222, causing the aspartic acid (D) at amino acid position 408 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