rs10939515

Variant names:

• chr4-9771672-G-A
• rs10939515
• XM_011513856.4:c.1619-303C>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: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508585.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000508585.5	TSL:3	n.182-303C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10939515;

hg19: chr4-9773296;