rs16890979
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020041.3(SLC2A9):c.844G>A(p.Val282Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,613,968 control chromosomes in the GnomAD database, including 46,504 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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.844G>A | p.Val282Ile | missense_variant | 7/12 | ENST00000264784.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A9 | ENST00000264784.8 | c.844G>A | p.Val282Ile | missense_variant | 7/12 | 1 | NM_020041.3 | A2 | |
SLC2A9 | ENST00000309065.7 | c.757G>A | p.Val253Ile | missense_variant | 8/13 | 1 | P2 | ||
SLC2A9 | ENST00000505104.5 | n.878G>A | non_coding_transcript_exon_variant | 8/12 | 1 | ||||
SLC2A9 | ENST00000506583.5 | c.757G>A | p.Val253Ile | missense_variant | 9/14 | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42936AN: 152072Hom.: 6956 Cov.: 33
GnomAD3 exomes AF: 0.243 AC: 61149AN: 251162Hom.: 8893 AF XY: 0.236 AC XY: 32097AN XY: 135816
GnomAD4 exome AF: 0.224 AC: 327053AN: 1461778Hom.: 39537 Cov.: 38 AF XY: 0.223 AC XY: 162344AN XY: 727190
GnomAD4 genome ? AF: 0.282 AC: 42983AN: 152190Hom.: 6967 Cov.: 33 AF XY: 0.279 AC XY: 20794AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | This variant is associated with the following publications: (PMID: 32514006, 18759275, 30315176, 29958533, 28508493, 18834626) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Hypouricemia, renal, 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 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. - |
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at