9-68384446-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021965.4(PGM5):c.473C>T(p.Thr158Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,604,748 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021965.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGM5 | ENST00000396396.6 | c.473C>T | p.Thr158Met | missense_variant | Exon 3 of 11 | 2 | NM_021965.4 | ENSP00000379678.1 | ||
PGM5 | ENST00000396392.5 | c.473C>T | p.Thr158Met | missense_variant | Exon 3 of 8 | 1 | ENSP00000379674.1 | |||
PGM5 | ENST00000431583.1 | c.323-3017C>T | intron_variant | Intron 2 of 3 | 5 | ENSP00000394864.1 | ||||
PGM5 | ENST00000604870.6 | n.828C>T | non_coding_transcript_exon_variant | Exon 6 of 12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000507 AC: 77AN: 151896Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250164Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135202
GnomAD4 exome AF: 0.0000702 AC: 102AN: 1452734Hom.: 1 Cov.: 27 AF XY: 0.0000816 AC XY: 59AN XY: 723168
GnomAD4 genome AF: 0.000507 AC: 77AN: 152014Hom.: 0 Cov.: 28 AF XY: 0.000511 AC XY: 38AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.473C>T (p.T158M) alteration is located in exon 3 (coding exon 3) of the PGM5 gene. This alteration results from a C to T substitution at nucleotide position 473, causing the threonine (T) at amino acid position 158 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