rs13148356

Variant names:

• chr4-9815446-G-A
• rs13148356
• ENST00000503280.5:n.420+10974C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503280.5(SLC2A9):​n.420+10974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,114 control chromosomes in the GnomAD database, including 21,243 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (21243 hom., cov: 33)
• Consequence: SLC2A9 ENST00000503280.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• hypouricemia, renal, 2

  Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	XM_011513856.4	c.1419+19435C>T		intron_variant	Intron 11 of 12		XP_011512158.1
SLC2A9	XM_017008457.3	c.1600+10974C>T		intron_variant	Intron 12 of 12		XP_016863946.1
SLC2A9	XM_011513858.2	c.1332+19435C>T		intron_variant	Intron 12 of 13		XP_011512160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000503280.5	n.420+10974C>T		intron_variant	Intron 3 of 3	4
SLC2A9	ENST00000503803.5	n.385+10974C>T		intron_variant	Intron 3 of 3	3
SLC2A9	ENST00000508585.5	n.181+10974C>T		intron_variant	Intron 1 of 1	3
SLC2A9	ENST00000512342.5	n.385+10974C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76820 AN: 151996 Hom.: 21238 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.516

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.505 AC: 76827 AN: 152114 Hom.: 21243 Cov.: 33 AF XY: 0.501 AC XY: 37261 AN XY: 74334

African (AFR) AF: 0.318 AC: 13205 AN: 41492

American (AMR) AF: 0.447 AC: 6823 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2282 AN: 3472

East Asian (EAS) AF: 0.181 AC: 934 AN: 5170

South Asian (SAS) AF: 0.455 AC: 2196 AN: 4828

European-Finnish (FIN) AF: 0.604 AC: 6388 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43261 AN: 68000

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.527 Hom.: 3618

Bravo AF: 0.485

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.93
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13148356; hg19: chr4-9817070;