7-44065189-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000290.4(PGAM2):āc.341T>Gā(p.Ile114Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 1,613,994 control chromosomes in the GnomAD database, including 827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM2 | ENST00000297283.4 | c.341T>G | p.Ile114Ser | missense_variant | Exon 1 of 3 | 1 | NM_000290.4 | ENSP00000297283.3 | ||
DBNL | ENST00000448521.6 | c.*4273A>C | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_001014436.3 | ENSP00000411701.1 |
Frequencies
GnomAD3 genomes AF: 0.0271 AC: 4129AN: 152088Hom.: 130 Cov.: 33
GnomAD3 exomes AF: 0.0273 AC: 6860AN: 251284Hom.: 250 AF XY: 0.0301 AC XY: 4089AN XY: 135866
GnomAD4 exome AF: 0.0148 AC: 21562AN: 1461788Hom.: 695 Cov.: 35 AF XY: 0.0170 AC XY: 12397AN XY: 727206
GnomAD4 genome AF: 0.0272 AC: 4146AN: 152206Hom.: 132 Cov.: 33 AF XY: 0.0282 AC XY: 2100AN XY: 74418
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Glycogen storage disease type X Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at