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):āc.286A>Gā(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 (ā ). 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 | Labcorp Genetics (formerly Invitae), Labcorp | 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