rs5028843

Variant names:

• chr4-9939182-G-A
• rs5028843
• NM_020041.3:c.814+2731C>T

Variant summary

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

The NM_020041.3(SLC2A9):​c.814+2731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,020 control chromosomes in the GnomAD database, including 9,271 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 0.32 (9271 hom., cov: 31)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. 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
	SLC2A9	NM_020041.3	MANE Select	c.814+2731C>T		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.727+2731C>T		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.814+2731C>T		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.727+2731C>T		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.848+2731C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49145 AN: 151902 Hom.: 9243 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.324 AC: 49227 AN: 152020 Hom.: 9271 Cov.: 31 AF XY: 0.321 AC XY: 23892 AN XY: 74328

African (AFR) AF: 0.505 AC: 20942 AN: 41434

American (AMR) AF: 0.394 AC: 6020 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3466

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5166

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4816

European-Finnish (FIN) AF: 0.218 AC: 2303 AN: 10580

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16639 AN: 67966

Other (OTH) AF: 0.306 AC: 644 AN: 2108

Alfa AF: 0.326 Hom.: 2045

Bravo AF: 0.343

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs5028843; hg19: chr4-9940806;