4-9796079-C-T

Variant names:

• chr4-9796079-C-T
• rs13106539
• ENST00000503803.5:n.386-16014G>A

Variant summary

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

The ENST00000503803.5(SLC2A9):​n.386-16014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,992 control chromosomes in the GnomAD database, including 22,178 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 0.52 (22178 hom., cov: 32)
• Consequence: SLC2A9 ENST00000503803.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 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	ENST00000503803.5	TSL:3	n.386-16014G>A		intron	N/A
	SLC2A9	ENST00000508585.5	TSL:3	n.182-24710G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79471 AN: 151874 Hom.: 22164 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.523 AC: 79505 AN: 151992 Hom.: 22178 Cov.: 32 AF XY: 0.518 AC XY: 38475 AN XY: 74282

African (AFR) AF: 0.379 AC: 15705 AN: 41466

American (AMR) AF: 0.454 AC: 6928 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2316 AN: 3462

East Asian (EAS) AF: 0.193 AC: 996 AN: 5172

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4818

European-Finnish (FIN) AF: 0.603 AC: 6354 AN: 10534

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43262 AN: 67950

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.592 Hom.: 67830

Bravo AF: 0.506

Asia WGS AF: 0.334 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.70
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs13106539; hg19: chr4-9797703;