chr12-7814369-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001286234.2(SLC2A14):​c.1441G>A​(p.Val481Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SLC2A14
NM_001286234.2 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0490
Variant links:
Genes affected
SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06506553).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A14NM_001286234.2 linkc.1441G>A p.Val481Ile missense_variant Exon 11 of 11 ENST00000431042.7 NP_001273163.1 Q8TDB8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A14ENST00000431042.7 linkc.1441G>A p.Val481Ile missense_variant Exon 11 of 11 1 NM_001286234.2 ENSP00000407287.2 Q8TDB8-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
2
AN:
149484
Hom.:
0
Cov.:
26
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000220
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000149
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
250976
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135676
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461526
Hom.:
0
Cov.:
69
AF XY:
0.00
AC XY:
0
AN XY:
727084
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000134
AC:
2
AN:
149484
Hom.:
0
Cov.:
26
AF XY:
0.0000138
AC XY:
1
AN XY:
72718
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000220
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000149
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Mar 01, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1510G>A (p.V504I) alteration is located in exon 12 (coding exon 10) of the SLC2A14 gene. This alteration results from a G to A substitution at nucleotide position 1510, causing the valine (V) at amino acid position 504 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.075
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
0.020
DANN
Benign
0.66
DEOGEN2
Benign
0.0062
.;.;T;T;.;.;T;.;.
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0029
N
LIST_S2
Benign
0.35
.;T;T;.;T;T;.;.;T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.065
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.79
T
MutationAssessor
Benign
0.0
.;.;N;N;.;.;N;.;.
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-0.35
N;N;.;N;N;N;N;N;N
REVEL
Benign
0.13
Sift
Benign
0.36
T;T;.;T;T;T;T;T;T
Sift4G
Benign
0.50
T;T;T;T;T;T;T;T;T
Polyphen
0.012
B;.;B;B;B;.;B;.;.
Vest4
0.017
MutPred
0.30
.;.;Gain of catalytic residue at V504 (P = 0.0107);Gain of catalytic residue at V504 (P = 0.0107);.;.;Gain of catalytic residue at V504 (P = 0.0107);.;.;
MVP
0.24
MPC
0.80
ClinPred
0.060
T
GERP RS
-2.5
Varity_R
0.028
gMVP
0.19

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1325643887; hg19: chr12-7966965; COSMIC: COSV61588795; API