rs1131596
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_194255.4(SLC19A1):c.-43C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,437,318 control chromosomes in the GnomAD database, including 221,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.50 ( 20155 hom., cov: 32)
Exomes 𝑓: 0.56 ( 201480 hom. )
Consequence
SLC19A1
NM_194255.4 5_prime_UTR
NM_194255.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.13
Genes affected
SLC19A1 (HGNC:10937): (solute carrier family 19 member 1) The membrane protein encoded by this gene is a transporter of folate and is involved in the regulation of intracellular concentrations of folate. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 21-45538002-G-A is Benign according to our data. Variant chr21-45538002-G-A is described in ClinVar as [Benign]. Clinvar id is 1220816.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC19A1 | NM_194255.4 | c.-43C>T | 5_prime_UTR_variant | 2/6 | ENST00000311124.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC19A1 | ENST00000311124.9 | c.-43C>T | 5_prime_UTR_variant | 2/6 | 1 | NM_194255.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.504 AC: 76469AN: 151792Hom.: 20135 Cov.: 32
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GnomAD3 exomes AF: 0.522 AC: 47113AN: 90294Hom.: 12320 AF XY: 0.528 AC XY: 24752AN XY: 46874
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GnomAD4 exome AF: 0.557 AC: 716515AN: 1285408Hom.: 201480 Cov.: 22 AF XY: 0.559 AC XY: 349314AN XY: 625410
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GnomAD4 genome ? AF: 0.504 AC: 76519AN: 151910Hom.: 20155 Cov.: 32 AF XY: 0.505 AC XY: 37521AN XY: 74230
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2019 | This variant is associated with the following publications: (PMID: 17404734, 18053808) - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
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