chr4-37840217-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_018290.4(PGM2):āc.677A>Gā(p.Asn226Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_018290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM2 | NM_018290.4 | c.677A>G | p.Asn226Ser | missense_variant | 6/14 | ENST00000381967.9 | |
PGM2 | XM_047415895.1 | c.260A>G | p.Asn87Ser | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2 | ENST00000381967.9 | c.677A>G | p.Asn226Ser | missense_variant | 6/14 | 1 | NM_018290.4 | P1 | |
PGM2 | ENST00000515668.5 | c.*256A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 1 | ||||
PGM2 | ENST00000505986.5 | c.*256A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/11 | 2 | ||||
PGM2 | ENST00000512556.1 | c.*214A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460606Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726750
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | PGM2: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at