rs13129697

Variant names:

• chr4-9925343-T-G
• rs13129697
• NM_020041.3:c.815-4771A>C

Variant summary

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

The NM_020041.3(SLC2A9):​c.815-4771A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,050 control chromosomes in the GnomAD database, including 13,167 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 0.39 (13167 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 58 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.815-4771A>C		intron_variant	Intron 6 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.815-4771A>C		intron_variant	Intron 6 of 11	1	NM_020041.3	ENSP00000264784.3
SLC2A9	ENST00000309065.7	c.728-4771A>C		intron_variant	Intron 7 of 12	1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.849-4771A>C		intron_variant	Intron 7 of 11	1
SLC2A9	ENST00000506583.5	c.728-4771A>C		intron_variant	Intron 8 of 13	5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59498 AN: 151932 Hom.: 13132 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.392 AC: 59600 AN: 152050 Hom.: 13167 Cov.: 33 AF XY: 0.396 AC XY: 29406 AN XY: 74322

African (AFR) AF: 0.584 AC: 24214 AN: 41438

American (AMR) AF: 0.477 AC: 7293 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2482 AN: 5156

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4808

European-Finnish (FIN) AF: 0.273 AC: 2887 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18421 AN: 67992

Other (OTH) AF: 0.371 AC: 782 AN: 2108

Alfa AF: 0.317 Hom.: 29317

Bravo AF: 0.414

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.7
DANN	Benign	0.86
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13129697; hg19: chr4-9926967;