15-84905644-C-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004213.5(SLC28A1):c.709C>A(p.Gln237Lys) variant causes a missense change. The variant allele was found at a frequency of 0.25 in 1,608,760 control chromosomes in the GnomAD database, including 53,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.23 ( 4358 hom., cov: 33)
Exomes 𝑓: 0.25 ( 49387 hom. )
Consequence
SLC28A1
NM_004213.5 missense
NM_004213.5 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 5.80
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005893916).
BP6
Variant 15-84905644-C-A is Benign according to our data. Variant chr15-84905644-C-A is described in ClinVar as [Benign]. Clinvar id is 3059004.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.709C>A | p.Gln237Lys | missense_variant | 8/19 | ENST00000394573.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.709C>A | p.Gln237Lys | missense_variant | 8/19 | 1 | NM_004213.5 | P1 | |
SLC28A1 | ENST00000286749.3 | c.709C>A | p.Gln237Lys | missense_variant | 7/18 | 1 | P1 | ||
SLC28A1 | ENST00000538177.5 | c.709C>A | p.Gln237Lys | missense_variant | 7/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.230 AC: 34972AN: 151980Hom.: 4345 Cov.: 33
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GnomAD3 exomes AF: 0.281 AC: 70544AN: 251152Hom.: 11327 AF XY: 0.281 AC XY: 38166AN XY: 135738
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GnomAD4 exome AF: 0.252 AC: 366592AN: 1456662Hom.: 49387 Cov.: 31 AF XY: 0.256 AC XY: 185300AN XY: 724882
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GnomAD4 genome AF: 0.230 AC: 35018AN: 152098Hom.: 4358 Cov.: 33 AF XY: 0.235 AC XY: 17455AN XY: 74354
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC28A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 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
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
D;P;P
Vest4
MPC
0.49
ClinPred
T
GERP RS
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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