chr17-38735314-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007144.3(PCGF2):c.944G>A(p.Gly315Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000326 in 1,534,022 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G315R) has been classified as Uncertain significance.
Frequency
Consequence
NM_007144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCGF2 | NM_007144.3 | c.944G>A | p.Gly315Glu | missense_variant | 11/11 | ENST00000620225.5 | |
CISD3 | NM_001136498.2 | c.*1859C>T | 3_prime_UTR_variant | 4/4 | ENST00000613478.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCGF2 | ENST00000620225.5 | c.944G>A | p.Gly315Glu | missense_variant | 11/11 | 1 | NM_007144.3 | P1 | |
CISD3 | ENST00000613478.2 | c.*1859C>T | 3_prime_UTR_variant | 4/4 | 2 | NM_001136498.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 32
GnomAD4 exome AF: 7.24e-7 AC: 1AN: 1381898Hom.: 0 Cov.: 33 AF XY: 0.00000148 AC XY: 1AN XY: 677608
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 315 of the PCGF2 protein (p.Gly315Glu). This variant has not been reported in the literature in individuals affected with PCGF2-related conditions. 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. ClinVar contains an entry for this variant (Variation ID: 1478692). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at