4-9786311-G-A

Variant names:

• chr4-9786311-G-A
• rs2867383
• ENST00000503803.5:n.386-6246C>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: 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	XM_011513856.4	c.1420-6246C>T		intron_variant	Intron 11 of 12		XP_011512158.1
SLC2A9	XM_017008457.3	c.1601-14942C>T		intron_variant	Intron 12 of 12		XP_016863946.1
SLC2A9	XM_011513858.2	c.1333-6246C>T		intron_variant	Intron 12 of 13		XP_011512160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000503803.5	n.386-6246C>T		intron_variant	Intron 3 of 3	3
SLC2A9	ENST00000508585.5	n.182-14942C>T		intron_variant	Intron 1 of 1	3

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 v4.3

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

Other links and lift over

dbSNP: rs2867383; hg19: chr4-9787935;