7-44062808-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000290.4(PGAM2):c.718C>G(p.Arg240Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,886 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. R240Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGAM2 | NM_000290.4 | c.718C>G | p.Arg240Gly | missense_variant | 3/3 | ENST00000297283.4 | |
DBNL | NM_001014436.3 | c.*1892G>C | 3_prime_UTR_variant | 13/13 | ENST00000448521.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGAM2 | ENST00000297283.4 | c.718C>G | p.Arg240Gly | missense_variant | 3/3 | 1 | NM_000290.4 | P1 | |
DBNL | ENST00000448521.6 | c.*1892G>C | 3_prime_UTR_variant | 13/13 | 1 | NM_001014436.3 | P4 | ||
DBNL | ENST00000432854.5 | c.*1892G>C | 3_prime_UTR_variant | 11/11 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251404Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135886
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 2022 | The c.718C>G (p.R240G) alteration is located in exon 3 (coding exon 3) of the PGAM2 gene. This alteration results from a C to G substitution at nucleotide position 718, causing the arginine (R) at amino acid position 240 to be replaced by a glycine (G). 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