chr11-74351303-ACACTTTTTAT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_173582.6(PGM2L1):c.749+70_749+79del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00519 in 1,335,786 control chromosomes in the GnomAD database, including 291 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 165 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 126 hom. )
Consequence
PGM2L1
NM_173582.6 intron
NM_173582.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.54
Genes affected
PGM2L1 (HGNC:20898): (phosphoglucomutase 2 like 1) Enables glucose-1,6-bisphosphate synthase activity. Predicted to be involved in glucose metabolic process and phosphorylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 11-74351303-ACACTTTTTAT-A is Benign according to our data. Variant chr11-74351303-ACACTTTTTAT-A is described in ClinVar as [Benign]. Clinvar id is 1268532.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM2L1 | NM_173582.6 | c.749+70_749+79del | intron_variant | ENST00000298198.5 | |||
LOC112268078 | XR_002957258.2 | n.315-16751_315-16742del | intron_variant, non_coding_transcript_variant | ||||
PGM2L1 | XM_011544953.4 | c.812+70_812+79del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2L1 | ENST00000298198.5 | c.749+70_749+79del | intron_variant | 1 | NM_173582.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0254 AC: 3859AN: 152194Hom.: 164 Cov.: 32
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GnomAD4 exome AF: 0.00259 AC: 3063AN: 1183474Hom.: 126 AF XY: 0.00228 AC XY: 1363AN XY: 597078
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GnomAD4 genome ? AF: 0.0254 AC: 3871AN: 152312Hom.: 165 Cov.: 32 AF XY: 0.0241 AC XY: 1793AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at