4-9789088-T-C

Variant names:

• chr4-9789088-T-C
• rs1850744
• ENST00000503803.5:n.386-9023A>G

Variant summary

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

The ENST00000503803.5(SLC2A9):​n.386-9023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 152,258 control chromosomes in the GnomAD database, including 66,376 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 0.93 (66376 hom., cov: 32)
• Consequence: SLC2A9 ENST00000503803.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 14 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000503803.5	TSL:3	n.386-9023A>G		intron	N/A
	SLC2A9	ENST00000508585.5	TSL:3	n.182-17719A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141869 AN: 152140 Hom.: 66312 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.933 AC: 141991 AN: 152258 Hom.: 66376 Cov.: 32 AF XY: 0.931 AC XY: 69267 AN XY: 74438

African (AFR) AF: 0.924 AC: 38357 AN: 41534

American (AMR) AF: 0.896 AC: 13701 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4194 AN: 5170

South Asian (SAS) AF: 0.841 AC: 4052 AN: 4820

European-Finnish (FIN) AF: 0.968 AC: 10272 AN: 10612

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64986 AN: 68038

Other (OTH) AF: 0.937 AC: 1983 AN: 2116

Alfa AF: 0.945 Hom.: 158649

Bravo AF: 0.927

Asia WGS AF: 0.832 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.53
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1850744; hg19: chr4-9790712;