7-141555492-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_018238.4(AGK):c.26G>A(p.Arg9Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000587 in 1,613,832 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R9P) has been classified as Uncertain significance.
Frequency
Consequence
NM_018238.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGK | NM_018238.4 | c.26G>A | p.Arg9Gln | missense_variant | 2/16 | ENST00000649286.2 | |
AGK | NM_001364948.3 | c.26G>A | p.Arg9Gln | missense_variant | 2/15 | ||
AGK | XM_011516397.4 | c.26G>A | p.Arg9Gln | missense_variant | 2/16 | ||
AGK | XM_024446835.2 | c.26G>A | p.Arg9Gln | missense_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGK | ENST00000649286.2 | c.26G>A | p.Arg9Gln | missense_variant | 2/16 | NM_018238.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 264AN: 251248Hom.: 1 AF XY: 0.00146 AC XY: 198AN XY: 135780
GnomAD4 exome AF: 0.000608 AC: 889AN: 1461642Hom.: 6 Cov.: 30 AF XY: 0.000916 AC XY: 666AN XY: 727114
GnomAD4 genome AF: 0.000388 AC: 59AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74390
ClinVar
Submissions by phenotype
Sengers syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
AGK-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Sengers syndrome;C3553494:Cataract 38 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | - - |
Cataract 38 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at