rs45584739
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004213.5(SLC28A1):āc.1636T>Cā(p.Ser546Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000617 in 1,613,988 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0035 ( 6 hom., cov: 33)
Exomes š: 0.00032 ( 6 hom. )
Consequence
SLC28A1
NM_004213.5 missense
NM_004213.5 missense
Scores
2
8
7
Clinical Significance
Conservation
PhyloP100: 6.12
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.018100917).
BP6
?
Variant 15-84943499-T-C is Benign according to our data. Variant chr15-84943499-T-C is described in ClinVar as [Benign]. Clinvar id is 634887.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.1636T>C | p.Ser546Pro | missense_variant | 16/19 | ENST00000394573.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.1636T>C | p.Ser546Pro | missense_variant | 16/19 | 1 | NM_004213.5 | P1 | |
SLC28A1 | ENST00000286749.3 | c.1636T>C | p.Ser546Pro | missense_variant | 15/18 | 1 | P1 | ||
SLC28A1 | ENST00000538177.5 | c.1138T>C | p.Ser380Pro | missense_variant | 12/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00346 AC: 526AN: 152174Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.000863 AC: 217AN: 251480Hom.: 5 AF XY: 0.000486 AC XY: 66AN XY: 135916
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GnomAD4 exome AF: 0.000322 AC: 470AN: 1461696Hom.: 6 Cov.: 30 AF XY: 0.000263 AC XY: 191AN XY: 727158
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GnomAD4 genome ? AF: 0.00345 AC: 526AN: 152292Hom.: 6 Cov.: 33 AF XY: 0.00328 AC XY: 244AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | SLC28A1: BS1, BS2 - |
SLC28A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 24, 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). - |
Uridine-cytidineuria Other:1
Affects, no assertion criteria provided | literature only | OMIM | Jun 18, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;.
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Benign
T;D;D
Sift4G
Uncertain
D;D;D
Polyphen
P;D;D
Vest4
MVP
MPC
0.49
ClinPred
T
GERP RS
Varity_R
gMVP
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