chr9-68387534-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_021965.4(PGM5):c.643G>A(p.Gly215Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000393 in 145,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021965.4 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 |
---|---|---|---|---|---|---|---|
PGM5 | NM_021965.4 | c.643G>A | p.Gly215Ser | missense_variant | 4/11 | ENST00000396396.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM5 | ENST00000396396.6 | c.643G>A | p.Gly215Ser | missense_variant | 4/11 | 2 | NM_021965.4 | P1 | |
PGM5 | ENST00000396392.5 | c.643G>A | p.Gly215Ser | missense_variant | 4/8 | 1 | |||
PGM5 | ENST00000431583.1 | c.394G>A | p.Gly132Ser | missense_variant | 3/4 | 5 | |||
PGM5 | ENST00000604870.6 | n.998G>A | non_coding_transcript_exon_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000393 AC: 57AN: 144906Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250870Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135578
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000133 AC: 188AN: 1414160Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 95AN XY: 704722
GnomAD4 genome ? AF: 0.000393 AC: 57AN: 145022Hom.: 0 Cov.: 32 AF XY: 0.000397 AC XY: 28AN XY: 70594
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at