chr1-63631673-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002633.3(PGM1):c.573G>T(p.Ser191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S191S) has been classified as Likely benign.
Frequency
Consequence
NM_002633.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.573G>T | p.Ser191= | synonymous_variant | 4/11 | ENST00000371084.8 | |
PGM1 | NM_001172818.1 | c.627G>T | p.Ser209= | synonymous_variant | 4/11 | ||
PGM1 | NM_001172819.2 | c.-19G>T | 5_prime_UTR_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084.8 | c.573G>T | p.Ser191= | synonymous_variant | 4/11 | 1 | NM_002633.3 | P1 | |
PGM1 | ENST00000650546.1 | c.573G>T | p.Ser191= | synonymous_variant | 4/12 | ||||
PGM1 | ENST00000371083.4 | c.627G>T | p.Ser209= | synonymous_variant | 4/11 | 2 | |||
PGM1 | ENST00000540265.5 | c.-19G>T | 5_prime_UTR_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at