rs78558135
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002863.5(PYGL):āc.2534A>Gā(p.Asn845Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00311 in 1,612,492 control chromosomes in the GnomAD database, including 140 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_002863.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYGL | NM_002863.5 | c.2534A>G | p.Asn845Ser | missense_variant | 20/20 | ENST00000216392.8 | |
PYGL | NM_001163940.2 | c.2432A>G | p.Asn811Ser | missense_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYGL | ENST00000216392.8 | c.2534A>G | p.Asn845Ser | missense_variant | 20/20 | 1 | NM_002863.5 | P1 | |
PYGL | ENST00000532462.5 | c.2379+2869A>G | intron_variant | 1 | |||||
PYGL | ENST00000544180.6 | c.2432A>G | p.Asn811Ser | missense_variant | 19/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0161 AC: 2444AN: 152204Hom.: 67 Cov.: 33
GnomAD3 exomes AF: 0.00397 AC: 998AN: 251346Hom.: 28 AF XY: 0.00294 AC XY: 399AN XY: 135842
GnomAD4 exome AF: 0.00175 AC: 2560AN: 1460170Hom.: 72 Cov.: 33 AF XY: 0.00155 AC XY: 1123AN XY: 726518
GnomAD4 genome ? AF: 0.0161 AC: 2452AN: 152322Hom.: 68 Cov.: 33 AF XY: 0.0151 AC XY: 1128AN XY: 74498
ClinVar
Submissions by phenotype
Glycogen storage disease, type VI Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 08, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | May 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at