chr5-151284048-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_181774.4(SLC36A3):āc.970T>Cā(p.Cys324Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,610,328 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.000012 ( 0 hom. )
Consequence
SLC36A3
NM_181774.4 missense
NM_181774.4 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 8.42
Genes affected
SLC36A3 (HGNC:19659): (solute carrier family 36 member 3) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transport and proton transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC36A3 | NM_181774.4 | c.970T>C | p.Cys324Arg | missense_variant | 8/10 | ENST00000335230.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A3 | ENST00000335230.8 | c.970T>C | p.Cys324Arg | missense_variant | 8/10 | 1 | NM_181774.4 | P1 | |
SLC36A3 | ENST00000377713.3 | c.1093T>C | p.Cys365Arg | missense_variant | 9/11 | 1 | |||
SLC36A3 | ENST00000423071.2 | n.2870T>C | non_coding_transcript_exon_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000284 AC: 7AN: 246366Hom.: 0 AF XY: 0.0000451 AC XY: 6AN XY: 133158
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1458136Hom.: 0 Cov.: 33 AF XY: 0.0000152 AC XY: 11AN XY: 725356
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.1093T>C (p.C365R) alteration is located in exon 9 (coding exon 9) of the SLC36A3 gene. This alteration results from a T to C substitution at nucleotide position 1093, causing the cysteine (C) at amino acid position 365 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Loss of catalytic residue at W325 (P = 0.0072);.;
MVP
MPC
0.28
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -24
Find out detailed SpliceAI scores and Pangolin per-transcript scores at