chr17-38735242-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007144.3(PCGF2):c.1016C>T(p.Pro339Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000443 in 1,445,602 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. P339P) has been classified as Likely benign.
Frequency
Consequence
NM_007144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCGF2 | NM_007144.3 | c.1016C>T | p.Pro339Leu | missense_variant | 11/11 | ENST00000620225.5 | |
CISD3 | NM_001136498.2 | c.*1787G>A | 3_prime_UTR_variant | 4/4 | ENST00000613478.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCGF2 | ENST00000620225.5 | c.1016C>T | p.Pro339Leu | missense_variant | 11/11 | 1 | NM_007144.3 | P1 | |
CISD3 | ENST00000613478.2 | c.*1787G>A | 3_prime_UTR_variant | 4/4 | 2 | NM_001136498.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000111 AC: 1AN: 90172Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 45344
GnomAD4 exome AF: 0.0000456 AC: 59AN: 1293418Hom.: 0 Cov.: 33 AF XY: 0.0000447 AC XY: 28AN XY: 626696
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with PCGF2-related conditions. This variant is present in population databases (rs760680898, gnomAD 0.003%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 339 of the PCGF2 protein (p.Pro339Leu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at