rs4849091
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_005415.5(SLC20A1):c.303G>A(p.Leu101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,613,440 control chromosomes in the GnomAD database, including 233,255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.44 ( 16545 hom., cov: 31)
Exomes 𝑓: 0.54 ( 216710 hom. )
Consequence
SLC20A1
NM_005415.5 synonymous
NM_005415.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.900
Genes affected
SLC20A1 (HGNC:10946): (solute carrier family 20 member 1) The protein encoded by this gene is a sodium-phosphate symporter that absorbs phosphate from interstitial fluid for use in cellular functions such as metabolism, signal transduction, and nucleic acid and lipid synthesis. The encoded protein is also a retroviral receptor, causing human cells to be susceptible to infection by gibbon ape leukemia virus, simian sarcoma-associated virus, feline leukemia virus subgroup B, and 10A1 murine leukemia virus.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 2-112647131-G-A is Benign according to our data. Variant chr2-112647131-G-A is described in ClinVar as [Benign]. Clinvar id is 3058938.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.9 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC20A1 | NM_005415.5 | c.303G>A | p.Leu101= | synonymous_variant | 2/11 | ENST00000272542.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC20A1 | ENST00000272542.8 | c.303G>A | p.Leu101= | synonymous_variant | 2/11 | 1 | NM_005415.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.438 AC: 66562AN: 151908Hom.: 16541 Cov.: 31
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GnomAD3 exomes AF: 0.493 AC: 123453AN: 250338Hom.: 32341 AF XY: 0.503 AC XY: 68105AN XY: 135440
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GnomAD4 exome AF: 0.537 AC: 785014AN: 1461414Hom.: 216710 Cov.: 53 AF XY: 0.538 AC XY: 390905AN XY: 726958
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GnomAD4 genome ? AF: 0.438 AC: 66585AN: 152026Hom.: 16545 Cov.: 31 AF XY: 0.438 AC XY: 32546AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC20A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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
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Name
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at