chr12-7814369-C-A

Variant names:

• chr12-7814369-C-A
• rs1325643887
• NM_001286234.2:c.1441G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001286234.2(SLC2A14):​c.1441G>T​(p.Val481Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V481I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000067 (0 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: SLC2A14 NM_001286234.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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]

ACMG classification

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=0.08967531).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A14	NM_001286234.2	c.1441G>T	p.Val481Phe	missense_variant	Exon 11 of 11	ENST00000431042.7	NP_001273163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A14	ENST00000431042.7	c.1441G>T	p.Val481Phe	missense_variant	Exon 11 of 11	1	NM_001286234.2	ENSP00000407287.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 149486 Hom.: 0 Cov.: 26 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000692

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 69

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000669 AC: 1 AN: 149486 Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0 AN XY: 72718

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000692

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.097	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	0.14
DANN	Benign	0.97
DEOGEN2	Benign	0.0098	.;.;T;T;.;.;T;.;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.052	N
LIST_S2	Benign	0.71	.;T;T;.;T;T;.;.;T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.090	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.59	T
MutationAssessor	Benign	0.0	.;.;N;N;.;.;N;.;.
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-0.50	N;N;.;N;N;N;N;N;N
REVEL	Benign	0.18
Sift	Uncertain	0.019	D;D;.;D;D;D;D;D;D
Sift4G	Uncertain	0.054	T;D;D;D;T;D;D;D;D
Polyphen		0.86	P;.;B;B;P;.;B;.;.
Vest4		0.11
MutPred		0.28		.;.;Gain of catalytic residue at N508 (P = 0.0483);Gain of catalytic residue at N508 (P = 0.0483);.;.;Gain of catalytic residue at N508 (P = 0.0483);.;.;
MVP		0.19
MPC		1.3
ClinPred		0.12	T
GERP RS		-2.5
Varity_R		0.081
gMVP		0.44

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

Other links and lift over

dbSNP: rs1325643887; hg19: chr12-7966965;