chr4-37834613-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018290.4(PGM2):c.250-5T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,395,466 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018290.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM2 | NM_018290.4 | c.250-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000381967.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2 | ENST00000381967.9 | c.250-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018290.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 392AN: 152226Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00263 AC: 640AN: 243738Hom.: 4 AF XY: 0.00291 AC XY: 383AN XY: 131798
GnomAD4 exome AF: 0.00271 AC: 3372AN: 1243122Hom.: 25 Cov.: 17 AF XY: 0.00292 AC XY: 1839AN XY: 629474
GnomAD4 genome AF: 0.00258 AC: 393AN: 152344Hom.: 2 Cov.: 32 AF XY: 0.00255 AC XY: 190AN XY: 74496
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, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at