chr4-9815446-G-A

Variant names:

• chr4-9815446-G-A
• rs13148356
• XM_011513856.4:c.1419+19435C>T

Variant summary

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

The ENST00000503803.5(SLC2A9):​n.385+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 ENST00000503803.5 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503803.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000503280.5	TSL:4	n.420+10974C>T		intron	N/A
	SLC2A9	ENST00000503803.5	TSL:3	n.385+10974C>T		intron	N/A
	SLC2A9	ENST00000508585.5	TSL:3	n.181+10974C>T		intron	N/A

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 v4.9

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;