chr11-93162716-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152313.4(SLC36A4):āc.1027C>Gā(p.Gln343Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000023 in 1,608,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 32)
Exomes š: 0.000014 ( 0 hom. )
Consequence
SLC36A4
NM_152313.4 missense
NM_152313.4 missense
Scores
1
3
15
Clinical Significance
Conservation
PhyloP100: 6.93
Genes affected
SLC36A4 (HGNC:19660): (solute carrier family 36 member 4) SLC36A4 belongs to the SLC36 family of amino acid transporters based on sequence similarity with other family members (e.g., SLC36A1; MIM 606561). SLC36 proteins contain about 500 amino acids and have 9 to 11 transmembrane domains. Unlike other SLC36 family members, which are proton-coupled amino acid transporters, SLC36A4 is a high-affinity/low-capacity non-proton-coupled amino acid transporter (Pillai and Meredith, 2011 [PubMed 21097500]).[supplied by OMIM, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19904792).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC36A4 | NM_152313.4 | c.1027C>G | p.Gln343Glu | missense_variant | 9/11 | ENST00000326402.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A4 | ENST00000326402.9 | c.1027C>G | p.Gln343Glu | missense_variant | 9/11 | 1 | NM_152313.4 | P1 | |
SLC36A4 | ENST00000529184.5 | c.622C>G | p.Gln208Glu | missense_variant | 9/11 | 2 | |||
SLC36A4 | ENST00000534116.1 | c.709C>G | p.Gln237Glu | missense_variant | 6/7 | 3 | |||
SLC36A4 | ENST00000526735.1 | n.1773C>G | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152074Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247444Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133878
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GnomAD4 exome AF: 0.0000144 AC: 21AN: 1455960Hom.: 0 Cov.: 29 AF XY: 0.0000179 AC XY: 13AN XY: 724402
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GnomAD4 genome AF: 0.000105 AC: 16AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74276
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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 | Dec 15, 2023 | The c.1027C>G (p.Q343E) alteration is located in exon 9 (coding exon 9) of the SLC36A4 gene. This alteration results from a C to G substitution at nucleotide position 1027, causing the glutamine (Q) at amino acid position 343 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MutPred
Loss of helix (P = 0.0626);.;.;
MVP
MPC
ClinPred
T
GERP RS
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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