5-55645869-T-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_173514.4(SLC38A9):c.1087A>T(p.Thr363Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000525 in 1,610,042 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00054 ( 6 hom. )
Consequence
SLC38A9
NM_173514.4 missense
NM_173514.4 missense
Scores
1
1
15
Clinical Significance
Conservation
PhyloP100: 7.63
Genes affected
SLC38A9 (HGNC:26907): (solute carrier family 38 member 9) Enables L-arginine transmembrane transporter activity and L-leucine transmembrane transporter activity. Involved in amino acid transmembrane transport; cellular response to amino acid stimulus; and positive regulation of TOR signaling. Located in late endosome and lysosomal membrane. Is integral component of lysosomal membrane. Colocalizes with Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.013620943).
BP6
Variant 5-55645869-T-A is Benign according to our data. Variant chr5-55645869-T-A is described in ClinVar as [Benign]. Clinvar id is 731355.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC38A9 | NM_173514.4 | c.1087A>T | p.Thr363Ser | missense_variant | 12/16 | ENST00000396865.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A9 | ENST00000396865.7 | c.1087A>T | p.Thr363Ser | missense_variant | 12/16 | 1 | NM_173514.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152148Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00108 AC: 266AN: 247372Hom.: 1 AF XY: 0.000973 AC XY: 130AN XY: 133550
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GnomAD4 exome AF: 0.000539 AC: 786AN: 1457776Hom.: 6 Cov.: 29 AF XY: 0.000549 AC XY: 398AN XY: 724986
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GnomAD4 genome AF: 0.000394 AC: 60AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74454
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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 | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L;.;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
B;.;B;.;.;.
Vest4
MutPred
Loss of sheet (P = 0.1158);.;Loss of sheet (P = 0.1158);.;.;.;
MVP
MPC
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T
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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