chr11-74342575-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The NM_173582.6(PGM2L1):c.1518G>T(p.Arg506Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 1,605,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_173582.6 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 |
---|---|---|---|---|---|---|---|
PGM2L1 | NM_173582.6 | c.1518G>T | p.Arg506Ser | missense_variant | 12/14 | ENST00000298198.5 | |
LOC112268078 | XR_002957258.2 | n.314+13087C>A | intron_variant, non_coding_transcript_variant | ||||
PGM2L1 | XM_011544953.4 | c.1581G>T | p.Arg527Ser | missense_variant | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2L1 | ENST00000298198.5 | c.1518G>T | p.Arg506Ser | missense_variant | 12/14 | 1 | NM_173582.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247236Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133688
GnomAD4 exome AF: 0.0000475 AC: 69AN: 1453602Hom.: 0 Cov.: 32 AF XY: 0.0000470 AC XY: 34AN XY: 723060
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2021 | The c.1518G>T (p.R506S) alteration is located in exon 12 (coding exon 12) of the PGM2L1 gene. This alteration results from a G to T substitution at nucleotide position 1518, causing the arginine (R) at amino acid position 506 to be replaced by a serine (S). 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