10-70884002-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_000281.4(PCBD1):c.263G>A(p.Arg88Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,614,100 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCBD1 | NM_000281.4 | c.263G>A | p.Arg88Gln | missense_variant | Exon 4 of 4 | ENST00000299299.4 | NP_000272.1 | |
PCBD1 | NM_001289797.2 | c.116G>A | p.Arg39Gln | missense_variant | Exon 4 of 4 | NP_001276726.1 | ||
PCBD1 | NM_001323004.2 | c.216+1150G>A | intron_variant | Intron 3 of 3 | NP_001309933.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000756 AC: 115AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000275 AC: 69AN: 251258Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135802
GnomAD4 exome AF: 0.000104 AC: 152AN: 1461826Hom.: 1 Cov.: 35 AF XY: 0.000105 AC XY: 76AN XY: 727206
GnomAD4 genome AF: 0.000788 AC: 120AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000819 AC XY: 61AN XY: 74458
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Pterin-4 alpha-carbinolamine dehydratase 1 deficiency Benign:1
- -
PCBD1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at