4-9923900-T-C

Variant names:

• chr4-9923900-T-C
• rs938552
• NM_020041.3:c.815-3328A>G

Variant summary

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

The NM_020041.3(SLC2A9):​c.815-3328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,092 control chromosomes in the GnomAD database, including 40,070 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 0.72 (40036 hom., cov: 31)
  • Exomes 𝑓: 0.80 (34 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 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

ENSG00000249219 (HGNC:40637):

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 (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. 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
	SLC2A9	NM_020041.3	MANE Select	c.815-3328A>G		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.728-3328A>G		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.815-3328A>G		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.728-3328A>G		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.849-3328A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109015 AN: 151868 Hom.: 40013 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.734

GnomAD4 exome AF: 0.802 AC: 85 AN: 106 Hom.: 34 Cov.: 0 AF XY: 0.769 AC XY: 60 AN XY: 78

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.800 AC: 16 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 50 AN: 60

Other (OTH) AF: 0.786 AC: 11 AN: 14

GnomAD4 genome AF: 0.718 AC: 109086 AN: 151986 Hom.: 40036 Cov.: 31 AF XY: 0.721 AC XY: 53516 AN XY: 74272

African (AFR) AF: 0.572 AC: 23696 AN: 41404

American (AMR) AF: 0.639 AC: 9764 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2604 AN: 3470

East Asian (EAS) AF: 0.981 AC: 5051 AN: 5148

South Asian (SAS) AF: 0.771 AC: 3717 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8664 AN: 10584

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53058 AN: 67960

Other (OTH) AF: 0.736 AC: 1554 AN: 2110

Alfa AF: 0.746 Hom.: 26527

Bravo AF: 0.700

Asia WGS AF: 0.847 AC: 2946 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	1.4
DANN	Benign	0.69
PhyloP100		-0.28
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: rs938552; hg19: chr4-9925524;