rs13113918

chr4-9996869-A-Cchr4-9996869-A-Gchr4-9996869-A-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_020041.3(SLC2A9):c.322T>G(p.Leu108Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L108L) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC2A9 NM_020041.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

Genes affected

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC2A9-AS1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.38178986).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.322T>G	p.Leu108Val	missense_variant	3/12	ENST00000264784.8
SLC2A9-AS1	NR_183861.1	n.308-2224A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.322T>G	p.Leu108Val	missense_variant	3/12	1	NM_020041.3	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000164 AC: 24 AN: 1461854 Hom.: 0 Cov.: 49 AF XY: 0.0000165 AC XY: 12 AN XY: 727234

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000453

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.0017	T
BayesDel_noAF	Benign	-0.24
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Benign	0.25	T;.;.;.
Eigen	Benign	0.18
Eigen_PC	Benign	0.21
FATHMM_MKL	Benign	0.47	N
LIST_S2	Uncertain	0.87	D;.;D;D
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.38	T;T;T;T
MetaSVM	Uncertain	-0.21	T
MutationAssessor	Benign	1.9	L;.;.;.
MutationTaster	Benign	0.43	P;P;P
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-2.2	N;N;N;N
REVEL	Uncertain	0.31
Sift	Benign	0.034	D;D;D;D
Sift4G	Benign	0.088	T;T;T;D
Polyphen		0.90	P;P;P;.
Vest4		0.20
MutPred		0.29		Loss of catalytic residue at L108 (P = 0.1333);.;.;.;
MVP		0.64
MPC		0.47
ClinPred		0.82	D
GERP RS		5.2
Varity_R		0.31
gMVP		0.33

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: rs13113918; hg19: chr4-9998493;