rs2867383

Variant names:

• chr4-9786311-G-A
• rs2867383
• XM_011513856.4:c.1420-6246C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-9786311-G-A
• chr4-9786311-G-T

Variant summary

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

The ENST00000503803.5(SLC2A9):​n.386-6246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,710 control chromosomes in the GnomAD database, including 10,216 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 0.36 (10216 hom., cov: 32)
• Consequence: SLC2A9 ENST00000503803.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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

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	ENST00000503803.5	TSL:3	n.386-6246C>T		intron	N/A
	SLC2A9	ENST00000508585.5	TSL:3	n.182-14942C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54903 AN: 151590 Hom.: 10197 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.362 AC: 54944 AN: 151710 Hom.: 10216 Cov.: 32 AF XY: 0.364 AC XY: 27008 AN XY: 74122

African (AFR) AF: 0.415 AC: 17168 AN: 41364

American (AMR) AF: 0.422 AC: 6443 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2783 AN: 5134

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4814

European-Finnish (FIN) AF: 0.354 AC: 3721 AN: 10498

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21133 AN: 67864

Other (OTH) AF: 0.364 AC: 766 AN: 2106

Alfa AF: 0.346 Hom.: 1145

Bravo AF: 0.372

Asia WGS AF: 0.421 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.57
PhyloP100		0.67

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: rs2867383;

hg19: chr4-9787935;