chr14-74946401-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002632.6(PGF):c.400C>T(p.Arg134Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,610,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002632.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGF | NM_002632.6 | c.400C>T | p.Arg134Trp | missense_variant | 5/7 | ENST00000555567.6 | |
LOC107984690 | XR_001750826.3 | n.2866G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGF | ENST00000555567.6 | c.400C>T | p.Arg134Trp | missense_variant | 5/7 | 1 | NM_002632.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000109 AC: 27AN: 248530Hom.: 0 AF XY: 0.0000969 AC XY: 13AN XY: 134222
GnomAD4 exome AF: 0.000107 AC: 156AN: 1458072Hom.: 0 Cov.: 33 AF XY: 0.000112 AC XY: 81AN XY: 724894
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.400C>T (p.R134W) alteration is located in exon 5 (coding exon 5) of the PGF gene. This alteration results from a C to T substitution at nucleotide position 400, causing the arginine (R) at amino acid position 134 to be replaced by a tryptophan (W). 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