rs75633423
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000164139.4(PYGM):c.661-5C>T 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 0.000054 in 1,612,040 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
ENST00000164139.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYGM | NM_005609.4 | c.661-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000164139.4 | NP_005600.1 | |||
PYGM | NM_001164716.1 | c.397-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001158188.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYGM | ENST00000164139.4 | c.661-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005609.4 | ENSP00000164139 | P1 | |||
PYGM | ENST00000377432.7 | c.397-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | ENSP00000366650 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249676Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135270
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1459784Hom.: 0 Cov.: 32 AF XY: 0.0000592 AC XY: 43AN XY: 726344
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74446
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at