14-74948547-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000555567.6(PGF):c.352G>A(p.Val118Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000033 in 1,604,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000555567.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGF | NM_002632.6 | c.352G>A | p.Val118Met | missense_variant | 4/7 | ENST00000555567.6 | NP_002623.2 | |
LOC107984690 | XR_001750826.3 | n.5012C>T | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGF | ENST00000555567.6 | c.352G>A | p.Val118Met | missense_variant | 4/7 | 1 | NM_002632.6 | ENSP00000451040 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248818Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134618
GnomAD4 exome AF: 0.0000275 AC: 40AN: 1452596Hom.: 0 Cov.: 30 AF XY: 0.0000277 AC XY: 20AN XY: 721042
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.352G>A (p.V118M) alteration is located in exon 4 (coding exon 4) of the PGF gene. This alteration results from a G to A substitution at nucleotide position 352, causing the valine (V) at amino acid position 118 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at