NM_020041.3:c.815-808C>A

Variant names:

• chr4-9921380-G-T
• rs734553
• NM_020041.3:c.815-808C>A

Variant summary

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

The NM_020041.3(SLC2A9):​c.815-808C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,000 control chromosomes in the GnomAD database, including 36,136 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 0.68 (36136 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 72 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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.815-808C>A		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.728-808C>A		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.815-808C>A		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.728-808C>A		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.849-808C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102650 AN: 151882 Hom.: 36135 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.676 AC: 102680 AN: 152000 Hom.: 36136 Cov.: 32 AF XY: 0.679 AC XY: 50410 AN XY: 74294

African (AFR) AF: 0.477 AC: 19742 AN: 41400

American (AMR) AF: 0.614 AC: 9379 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5065 AN: 5166

South Asian (SAS) AF: 0.744 AC: 3588 AN: 4822

European-Finnish (FIN) AF: 0.785 AC: 8301 AN: 10574

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51673 AN: 67976

Other (OTH) AF: 0.699 AC: 1470 AN: 2104

Alfa AF: 0.735 Hom.: 142131

Bravo AF: 0.656

Asia WGS AF: 0.826 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.022
DANN	Benign	0.45
PhyloP100		-1.4
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: rs734553; hg19: chr4-9923004;