4-9777956-C-T

Variant names:

• chr4-9777956-C-T
• rs10033951
• XM_006713968.5:c.*2018G>A

Variant summary

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

The XM_006713968.5(SLC2A9):​c.*2018G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,856 control chromosomes in the GnomAD database, including 10,092 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 (10092 hom., cov: 32)
• Consequence: SLC2A9 XM_006713968.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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

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	ENST00000508585.5	TSL:3	n.182-6587G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54306 AN: 151738 Hom.: 10075 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.358 AC: 54355 AN: 151856 Hom.: 10092 Cov.: 32 AF XY: 0.362 AC XY: 26817 AN XY: 74178

African (AFR) AF: 0.392 AC: 16224 AN: 41366

American (AMR) AF: 0.419 AC: 6411 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2962 AN: 5140

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4810

European-Finnish (FIN) AF: 0.355 AC: 3738 AN: 10522

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21150 AN: 67952

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.331 Hom.: 1041

Bravo AF: 0.364

Asia WGS AF: 0.474 AC: 1650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10033951; hg19: chr4-9779580;