rs6827754

Variant names:

• chr4-10016529-C-A
• rs6827754
• NM_020041.3:c.249+2446G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-10016529-C-A
• chr4-10016529-C-G
• chr4-10016529-C-T

Variant summary

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

The NM_020041.3(SLC2A9):​c.249+2446G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,700 control chromosomes in the GnomAD database, including 23,742 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 0.55 (23742 hom., cov: 30)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 17 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

LOC124900664 (HGNC:):

SLC2A9-AS1 (HGNC:59109):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.249+2446G>T		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.162+2446G>T		intron	N/A	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.249+2446G>T		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.162+2446G>T		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.283+2446G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83155 AN: 151582 Hom.: 23711 Cov.: 30

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.549 AC: 83231 AN: 151700 Hom.: 23742 Cov.: 30 AF XY: 0.555 AC XY: 41145 AN XY: 74098

African (AFR) AF: 0.398 AC: 16464 AN: 41322

American (AMR) AF: 0.594 AC: 9064 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4548 AN: 5132

South Asian (SAS) AF: 0.750 AC: 3602 AN: 4804

European-Finnish (FIN) AF: 0.599 AC: 6299 AN: 10512

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39269 AN: 67902

Other (OTH) AF: 0.557 AC: 1170 AN: 2102

Alfa AF: 0.564 Hom.: 14408

Bravo AF: 0.541

Asia WGS AF: 0.788 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.49
PhyloP100		-1.7
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: rs6827754; hg19: chr4-10018153;