12-224123-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_016615.5(SLC6A13):c.1180T>C(p.Cys394Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000249 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00026 ( 0 hom. )
Consequence
SLC6A13
NM_016615.5 missense
NM_016615.5 missense
Scores
7
5
5
Clinical Significance
Conservation
PhyloP100: 4.12
Genes affected
SLC6A13 (HGNC:11046): (solute carrier family 6 member 13) Enables amino acid transmembrane transporter activity and monocarboxylic acid transmembrane transporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.827
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A13 | NM_016615.5 | c.1180T>C | p.Cys394Arg | missense_variant | 11/15 | ENST00000343164.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A13 | ENST00000343164.9 | c.1180T>C | p.Cys394Arg | missense_variant | 11/15 | 1 | NM_016615.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152084Hom.: 0 Cov.: 33
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?
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GnomAD3 exomes AF: 0.000135 AC: 34AN: 251246Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135824
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GnomAD4 exome AF: 0.000257 AC: 376AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.000232 AC XY: 169AN XY: 727228
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GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74304
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ExAC
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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 | Oct 07, 2022 | The c.1180T>C (p.C394R) alteration is located in exon 11 (coding exon 10) of the SLC6A13 gene. This alteration results from a T to C substitution at nucleotide position 1180, causing the cysteine (C) at amino acid position 394 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
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.48
.;P
Vest4
MVP
MPC
0.55
ClinPred
D
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