rs938563

Variant names:

• chr4-9889374-G-C
• rs938563
• NM_020041.3:c.1215+1236C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-9889374-G-C
• chr4-9889374-G-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.1215+1236C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,086 control chromosomes in the GnomAD database, including 10,410 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 0.33 (10410 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.1215+1236C>G		intron_variant	Intron 9 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.1215+1236C>G		intron_variant	Intron 9 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50589 AN: 151968 Hom.: 10389 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.333 AC: 50658 AN: 152086 Hom.: 10410 Cov.: 33 AF XY: 0.332 AC XY: 24715 AN XY: 74360

African (AFR) AF: 0.562 AC: 23296 AN: 41486

American (AMR) AF: 0.410 AC: 6266 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2035 AN: 5146

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1834 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13967 AN: 67976

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.121 Hom.: 205

Bravo AF: 0.360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		0.13
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: rs938563; hg19: chr4-9890998;