chr12-121921510-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144668.6(CFAP251):c.205G>A(p.Asp69Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144668.6 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 |
---|---|---|---|---|---|---|---|
CFAP251 | NM_144668.6 | c.205G>A | p.Asp69Asn | missense_variant | 2/22 | ENST00000288912.9 | |
CFAP251 | NM_001178003.2 | c.205G>A | p.Asp69Asn | missense_variant | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP251 | ENST00000288912.9 | c.205G>A | p.Asp69Asn | missense_variant | 2/22 | 1 | NM_144668.6 | ||
CFAP251 | ENST00000397454.2 | c.205G>A | p.Asp69Asn | missense_variant | 2/18 | 1 | P1 | ||
CFAP251 | ENST00000540779.1 | n.103G>A | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152082Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 246158Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133574
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461538Hom.: 0 Cov.: 67 AF XY: 0.0000110 AC XY: 8AN XY: 727066
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152082Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.205G>A (p.D69N) alteration is located in exon 2 (coding exon 1) of the WDR66 gene. This alteration results from a G to A substitution at nucleotide position 205, causing the aspartic acid (D) at amino acid position 69 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