chr4-10039480-C-T

Variant names:

• chr4-10039480-C-T
• rs12508991
• ENST00000309065.7:c.-41+650G>A

Variant summary

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

The NM_001001290.2(SLC2A9):​c.-41+650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,148 control chromosomes in the GnomAD database, including 15,604 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 0.43 (15604 hom., cov: 33)
• Consequence: SLC2A9 NM_001001290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 13 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: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SLC2A9-AS1 (HGNC:59109):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001290.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_001001290.2		c.-41+650G>A		intron	N/A	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000309065.7	TSL:1	c.-41+650G>A		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.81+650G>A		intron	N/A
	SLC2A9	ENST00000506583.5	TSL:5	c.-41+650G>A		intron	N/A	ENSP00000422209.1	Q9NRM0-2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65295 AN: 152030 Hom.: 15599 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.429 AC: 65309 AN: 152148 Hom.: 15604 Cov.: 33 AF XY: 0.430 AC XY: 31991 AN XY: 74370

African (AFR) AF: 0.207 AC: 8613 AN: 41510

American (AMR) AF: 0.402 AC: 6143 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2191 AN: 5170

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4828

European-Finnish (FIN) AF: 0.523 AC: 5537 AN: 10578

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36562 AN: 67978

Other (OTH) AF: 0.444 AC: 939 AN: 2114

Alfa AF: 0.512 Hom.: 10062

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12508991; hg19: chr4-10041104;