rs950310

Variant names:

• chr4-9841226-T-A
• rs950310
• NM_020041.3:c.1292-6218A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-9841226-T-A
• chr4-9841226-T-C
• chr4-9841226-T-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.1292-6218A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,222 control chromosomes in the GnomAD database, including 2,682 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 0.18 (2682 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743
• Publications: 5 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 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.1292-6218A>T		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.1205-6218A>T		intron	N/A	NP_001001290.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.1292-6218A>T		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.1205-6218A>T		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000851832.1		c.1238-6218A>T		intron	N/A	ENSP00000521891.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28081 AN: 152104 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.185 AC: 28090 AN: 152222 Hom.: 2682 Cov.: 32 AF XY: 0.183 AC XY: 13624 AN XY: 74430

African (AFR) AF: 0.156 AC: 6500 AN: 41544

American (AMR) AF: 0.251 AC: 3842 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.150 AC: 779 AN: 5178

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10622

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 13013 AN: 67988

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.107 Hom.: 175

Bravo AF: 0.188

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.5
DANN	Benign	0.92
PhyloP100		0.74
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: rs950310; hg19: chr4-9842850;