rs10939515

Variant names:

• chr4-9771672-G-A
• rs10939515
• ENST00000508585.5:n.182-303C>T

Variant summary

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

The ENST00000508585.5(SLC2A9):​n.182-303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,228 control chromosomes in the GnomAD database, including 3,116 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 0.19 (3116 hom., cov: 34)
• Consequence: SLC2A9 ENST00000508585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	XM_011513856.4	c.1619-303C>T		intron_variant	Intron 12 of 12		XP_011512158.1
SLC2A9	XM_017008457.3	c.1601-303C>T		intron_variant	Intron 12 of 12		XP_016863946.1
SLC2A9	XM_011513858.2	c.1532-303C>T		intron_variant	Intron 13 of 13		XP_011512160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-303C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29639 AN: 152110 Hom.: 3110 Cov.: 34

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.195 AC: 29660 AN: 152228 Hom.: 3116 Cov.: 34 AF XY: 0.196 AC XY: 14586 AN XY: 74438

African (AFR) AF: 0.238 AC: 9902 AN: 41522

American (AMR) AF: 0.205 AC: 3132 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1674 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1409 AN: 4814

European-Finnish (FIN) AF: 0.155 AC: 1645 AN: 10608

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10707 AN: 68026

Other (OTH) AF: 0.186 AC: 393 AN: 2114

Alfa AF: 0.184 Hom.: 451

Bravo AF: 0.200

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.41
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10939515; hg19: chr4-9773296;