rs73520745
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000222248.4(SLC5A5):c.1507G>A(p.Asp503Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 1,569,392 control chromosomes in the GnomAD database, including 122 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 Likely benign (★★).
Frequency
Consequence
ENST00000222248.4 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 |
---|---|---|---|---|---|---|---|---|
SLC5A5 | NM_000453.3 | c.1507G>A | p.Asp503Asn | missense_variant | 12/15 | ENST00000222248.4 | NP_000444.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A5 | ENST00000222248.4 | c.1507G>A | p.Asp503Asn | missense_variant | 12/15 | 1 | NM_000453.3 | ENSP00000222248 | P1 | |
SLC5A5 | ENST00000597109.1 | n.506G>A | non_coding_transcript_exon_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0162 AC: 2466AN: 152192Hom.: 72 Cov.: 32
GnomAD3 exomes AF: 0.00381 AC: 659AN: 173058Hom.: 19 AF XY: 0.00297 AC XY: 280AN XY: 94122
GnomAD4 exome AF: 0.00168 AC: 2375AN: 1417082Hom.: 48 Cov.: 35 AF XY: 0.00144 AC XY: 1009AN XY: 701264
GnomAD4 genome AF: 0.0162 AC: 2472AN: 152310Hom.: 74 Cov.: 32 AF XY: 0.0158 AC XY: 1178AN XY: 74474
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 | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 11, 2016 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Thyroid dyshormonogenesis 1 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. - |
SLC5A5-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at