4-9908299-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020041.3(SLC2A9):c.1049C>T(p.Pro350Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 1,612,430 control chromosomes in the GnomAD database, including 199,977 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC2A9 | NM_020041.3 | c.1049C>T | p.Pro350Leu | missense_variant | 8/12 | ENST00000264784.8 | NP_064425.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC2A9 | ENST00000264784.8 | c.1049C>T | p.Pro350Leu | missense_variant | 8/12 | 1 | NM_020041.3 | ENSP00000264784 | A2 |
Frequencies
GnomAD3 genomes AF: 0.381 AC: 57795AN: 151858Hom.: 13725 Cov.: 31
GnomAD3 exomes AF: 0.442 AC: 111078AN: 251316Hom.: 26773 AF XY: 0.452 AC XY: 61334AN XY: 135824
GnomAD4 exome AF: 0.497 AC: 726551AN: 1460454Hom.: 186242 Cov.: 41 AF XY: 0.497 AC XY: 361048AN XY: 726644
GnomAD4 genome AF: 0.380 AC: 57814AN: 151976Hom.: 13735 Cov.: 31 AF XY: 0.381 AC XY: 28317AN XY: 74256
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | This variant is associated with the following publications: (PMID: 30315176) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hypouricemia, renal, 2 Benign:2
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 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 | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at