rs2269238
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_002633.3(PGM1):c.1464+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,609,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002633.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.1464+14G>A | intron_variant | Intron 9 of 10 | ENST00000371084.8 | NP_002624.2 | ||
PGM1 | NM_001172818.1 | c.1518+14G>A | intron_variant | Intron 9 of 10 | NP_001166289.1 | |||
PGM1 | NM_001172819.2 | c.873+14G>A | intron_variant | Intron 9 of 10 | NP_001166290.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251084Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135712
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1457822Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 725478
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74210
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
PGM1-congenital disorder of glycosylation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at