chr17-80101807-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The ENST00000390015.7(GAA):c.-112-4C>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 0.0014 in 152,324 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000390015.7 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
GAA | NM_000152.5 | c.-116C>T | 5_prime_UTR_variant | 1/20 | ENST00000302262.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAA | ENST00000302262.8 | c.-116C>T | 5_prime_UTR_variant | 1/20 | 1 | NM_000152.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00141 AC: 214AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 64Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 42
GnomAD4 genome ? AF: 0.00140 AC: 214AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74486
ClinVar
Submissions by phenotype
Glycogen storage disease, type II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 13, 2021 | The GAA c.-116C>T variant occurs in the 5' untranslated region. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is reported at a frequency of 0.004598 in the African/African American population of the Genome Aggregation Database (version 2.1.1). Based on the limited evidence, the c.-116C>T variant is classified as a variant of uncertain significance for glycogen storage disease type II. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at