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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	XM_006713968.5	c.*2018G>A		3_prime_UTR_variant	Exon 13 of 13		XP_006714031.1
SLC2A9	XM_047415974.1	c.*1867G>A		3_prime_UTR_variant	Exon 12 of 12		XP_047271930.1
SLC2A9	XM_047415977.1	c.*2018G>A		3_prime_UTR_variant	Exon 12 of 12		XP_047271933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-6587G>A		intron_variant	Intron 1 of 1	3

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 v4.3

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;