chr15-84905565-A-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004213.5(SLC28A1):c.630A>T(p.Gly210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,613,586 control chromosomes in the GnomAD database, including 365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.028 ( 200 hom., cov: 33)
Exomes 𝑓: 0.0029 ( 165 hom. )
Consequence
SLC28A1
NM_004213.5 synonymous
NM_004213.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.381
Genes affected
SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 15-84905565-A-T is Benign according to our data. Variant chr15-84905565-A-T is described in ClinVar as [Benign]. Clinvar id is 780006.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.381 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.092 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.630A>T | p.Gly210= | synonymous_variant | 8/19 | ENST00000394573.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.630A>T | p.Gly210= | synonymous_variant | 8/19 | 1 | NM_004213.5 | P1 | |
SLC28A1 | ENST00000286749.3 | c.630A>T | p.Gly210= | synonymous_variant | 7/18 | 1 | P1 | ||
SLC28A1 | ENST00000538177.5 | c.630A>T | p.Gly210= | synonymous_variant | 7/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0277 AC: 4211AN: 151978Hom.: 199 Cov.: 33
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GnomAD3 exomes AF: 0.00743 AC: 1869AN: 251454Hom.: 74 AF XY: 0.00527 AC XY: 716AN XY: 135910
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GnomAD4 exome AF: 0.00290 AC: 4245AN: 1461490Hom.: 165 Cov.: 31 AF XY: 0.00248 AC XY: 1804AN XY: 727078
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GnomAD4 genome AF: 0.0277 AC: 4211AN: 152096Hom.: 200 Cov.: 33 AF XY: 0.0269 AC XY: 2000AN XY: 74370
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
SLC28A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 26, 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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BayesDel_noAF
Benign
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at