chr7-134661692-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PP3_StrongPP5
The NM_001724.5(BPGM):c.185G>A(p.Arg62Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. R62R) has been classified as Likely benign.
Frequency
Consequence
NM_001724.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPGM | NM_001724.5 | c.185G>A | p.Arg62Gln | missense_variant | 2/3 | ENST00000344924.8 | |
LOC124901750 | XR_007060537.1 | n.29222-41744C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPGM | ENST00000344924.8 | c.185G>A | p.Arg62Gln | missense_variant | 2/3 | 1 | NM_001724.5 | P1 | |
BPGM | ENST00000393132.2 | c.185G>A | p.Arg62Gln | missense_variant | 3/4 | 5 | P1 | ||
BPGM | ENST00000418040.5 | c.185G>A | p.Arg62Gln | missense_variant | 3/4 | 5 | P1 | ||
BPGM | ENST00000443095.1 | c.185G>A | p.Arg62Gln | missense_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251214Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135766
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727216
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74304
ClinVar
Submissions by phenotype
Deficiency of bisphosphoglycerate mutase Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 17, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at