rs201805940
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_002633.3(PGM1):c.-41G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,612,102 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002633.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084 | c.-41G>A | 5_prime_UTR_variant | Exon 1 of 11 | 1 | NM_002633.3 | ENSP00000360125.3 | |||
PGM1 | ENST00000650546 | c.-41G>A | 5_prime_UTR_variant | Exon 1 of 12 | ENSP00000497812.1 | |||||
ITGB3BP | ENST00000478138.1 | n.197+77C>T | intron_variant | Intron 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 25AN: 241256Hom.: 0 AF XY: 0.0000680 AC XY: 9AN XY: 132402
GnomAD4 exome AF: 0.0000781 AC: 114AN: 1459838Hom.: 1 Cov.: 30 AF XY: 0.0000757 AC XY: 55AN XY: 726228
GnomAD4 genome AF: 0.000381 AC: 58AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74460
ClinVar
Submissions by phenotype
not provided 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at