chr10-70883979-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000281.4(PCBD1):c.286A>G(p.Ile96Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. I96I) has been classified as Likely benign.
Frequency
Consequence
NM_000281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCBD1 | NM_000281.4 | c.286A>G | p.Ile96Val | missense_variant | 4/4 | ENST00000299299.4 | |
PCBD1 | NM_001289797.2 | c.139A>G | p.Ile47Val | missense_variant | 4/4 | ||
PCBD1 | NM_001323004.2 | c.216+1173A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCBD1 | ENST00000299299.4 | c.286A>G | p.Ile96Val | missense_variant | 4/4 | 1 | NM_000281.4 | P1 | |
SGPL1 | ENST00000697988.1 | c.571-9780T>C | intron_variant | ||||||
PCBD1 | ENST00000493228.1 | n.685A>G | non_coding_transcript_exon_variant | 4/4 | 2 | ||||
PCBD1 | ENST00000493961.5 | n.183+1173A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461808Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727192
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Pterin-4 alpha-carbinolamine dehydratase 1 deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with PCBD1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 96 of the PCBD1 protein (p.Ile96Val). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at