chr21-45531642-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_194255.4(SLC19A1):c.696T>C(p.Pro232=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,611,988 control chromosomes in the GnomAD database, including 269,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 25021 hom., cov: 35)
Exomes 𝑓: 0.58 ( 244663 hom. )
Consequence
SLC19A1
NM_194255.4 synonymous
NM_194255.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.56
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 21-45531642-A-G is Benign according to our data. Variant chr21-45531642-A-G is described in ClinVar as [Benign]. Clinvar id is 1601263.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-6.56 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC19A1 | NM_194255.4 | c.696T>C | p.Pro232= | synonymous_variant | 3/6 | ENST00000311124.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC19A1 | ENST00000311124.9 | c.696T>C | p.Pro232= | synonymous_variant | 3/6 | 1 | NM_194255.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.572 AC: 86981AN: 152064Hom.: 24974 Cov.: 35
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GnomAD3 exomes AF: 0.578 AC: 142920AN: 247472Hom.: 41580 AF XY: 0.582 AC XY: 78349AN XY: 134530
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GnomAD4 exome AF: 0.578 AC: 843586AN: 1459806Hom.: 244663 Cov.: 76 AF XY: 0.580 AC XY: 421267AN XY: 726254
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GnomAD4 genome ? AF: 0.572 AC: 87084AN: 152182Hom.: 25021 Cov.: 35 AF XY: 0.571 AC XY: 42515AN XY: 74398
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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 | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at