chr11-74342507-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_173582.6(PGM2L1):c.1586G>A(p.Arg529Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000391 in 1,600,974 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R529W) has been classified as Uncertain significance.
Frequency
Consequence
NM_173582.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM2L1 | NM_173582.6 | c.1586G>A | p.Arg529Gln | missense_variant | 12/14 | ENST00000298198.5 | |
LOC112268078 | XR_002957258.2 | n.314+13019C>T | intron_variant, non_coding_transcript_variant | ||||
PGM2L1 | XM_011544953.4 | c.1649G>A | p.Arg550Gln | missense_variant | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2L1 | ENST00000298198.5 | c.1586G>A | p.Arg529Gln | missense_variant | 12/14 | 1 | NM_173582.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 151980Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 61AN: 242908Hom.: 0 AF XY: 0.000251 AC XY: 33AN XY: 131302
GnomAD4 exome AF: 0.000408 AC: 591AN: 1448892Hom.: 0 Cov.: 32 AF XY: 0.000412 AC XY: 297AN XY: 720218
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.1586G>A (p.R529Q) alteration is located in exon 12 (coding exon 12) of the PGM2L1 gene. This alteration results from a G to A substitution at nucleotide position 1586, causing the arginine (R) at amino acid position 529 to be replaced by a glutamine (Q). 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