chr9-68387468-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021965.4(PGM5):āc.577A>Gā(p.Ile193Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,457,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021965.4 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 |
---|---|---|---|---|---|---|---|
PGM5 | NM_021965.4 | c.577A>G | p.Ile193Val | missense_variant | 4/11 | ENST00000396396.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM5 | ENST00000396396.6 | c.577A>G | p.Ile193Val | missense_variant | 4/11 | 2 | NM_021965.4 | P1 | |
PGM5 | ENST00000396392.5 | c.577A>G | p.Ile193Val | missense_variant | 4/8 | 1 | |||
PGM5 | ENST00000431583.1 | c.328A>G | p.Ile110Val | missense_variant | 3/4 | 5 | |||
PGM5 | ENST00000604870.6 | n.932A>G | non_coding_transcript_exon_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250448Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135362
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1457978Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725488
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.577A>G (p.I193V) alteration is located in exon 4 (coding exon 4) of the PGM5 gene. This alteration results from a A to G substitution at nucleotide position 577, causing the isoleucine (I) at amino acid position 193 to be replaced by a valine (V). 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