rs60699980
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001024939.4(SLC2A11):c.1354G>A(p.Ala452Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0246 in 1,613,994 control chromosomes in the GnomAD database, including 589 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.032 ( 87 hom., cov: 32)
Exomes 𝑓: 0.024 ( 502 hom. )
Consequence
SLC2A11
NM_001024939.4 missense
NM_001024939.4 missense
Scores
4
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.15
Genes affected
SLC2A11 (HGNC:14239): (solute carrier family 2 member 11) This gene belongs to a family of proteins that mediate the transport of sugars across the cell membrane. The encoded protein transports glucose and fructose. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0027993321).
BA1
?
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A11 | NM_001024939.4 | c.1354G>A | p.Ala452Thr | missense_variant | 12/12 | ENST00000316185.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A11 | ENST00000316185.9 | c.1354G>A | p.Ala452Thr | missense_variant | 12/12 | 1 | NM_001024939.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0323 AC: 4914AN: 152064Hom.: 87 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0247 AC: 6219AN: 251342Hom.: 93 AF XY: 0.0244 AC XY: 3311AN XY: 135830
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GnomAD4 exome AF: 0.0238 AC: 34741AN: 1461812Hom.: 502 Cov.: 32 AF XY: 0.0238 AC XY: 17280AN XY: 727216
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GnomAD4 genome ? AF: 0.0323 AC: 4923AN: 152182Hom.: 87 Cov.: 32 AF XY: 0.0318 AC XY: 2363AN XY: 74388
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ALSPAC
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89
ESP6500AA
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206
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ExAC
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3005
Asia WGS
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;.;D
Vest4
MPC
0.41
ClinPred
T
GERP RS
Varity_R
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