rs73225891
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020041.3(SLC2A9):āc.841G>Cā(p.Asp281His) variant causes a missense change. The variant allele was found at a frequency of 0.0237 in 1,614,140 control chromosomes in the GnomAD database, including 568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. D281D) has been classified as Likely benign.
Frequency
Consequence
NM_020041.3 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 |
---|---|---|---|---|---|---|---|
SLC2A9 | NM_020041.3 | c.841G>C | p.Asp281His | missense_variant | 7/12 | ENST00000264784.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A9 | ENST00000264784.8 | c.841G>C | p.Asp281His | missense_variant | 7/12 | 1 | NM_020041.3 | A2 | |
SLC2A9 | ENST00000309065.7 | c.754G>C | p.Asp252His | missense_variant | 8/13 | 1 | P2 | ||
SLC2A9 | ENST00000505104.5 | n.875G>C | non_coding_transcript_exon_variant | 8/12 | 1 | ||||
SLC2A9 | ENST00000506583.5 | c.754G>C | p.Asp252His | missense_variant | 9/14 | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2853AN: 152196Hom.: 53 Cov.: 33
GnomAD3 exomes AF: 0.0198 AC: 4962AN: 251194Hom.: 77 AF XY: 0.0196 AC XY: 2669AN XY: 135838
GnomAD4 exome AF: 0.0242 AC: 35354AN: 1461826Hom.: 515 Cov.: 34 AF XY: 0.0237 AC XY: 17210AN XY: 727210
GnomAD4 genome ? AF: 0.0187 AC: 2852AN: 152314Hom.: 53 Cov.: 33 AF XY: 0.0192 AC XY: 1432AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 13, 2020 | This variant is associated with the following publications: (PMID: 25268603, 30315176) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Hypouricemia, renal, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at