NM_020041.3:c.1003-5881T>C

Variant names:

• chr4-9914226-A-G
• rs4697695
• NM_020041.3:c.1003-5881T>C

Variant summary

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

The NM_020041.3(SLC2A9):​c.1003-5881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,974 control chromosomes in the GnomAD database, including 35,095 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 (35095 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.1003-5881T>C		intron_variant	Intron 7 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.1003-5881T>C		intron_variant	Intron 7 of 11	1	NM_020041.3	ENSP00000264784.3
SLC2A9	ENST00000309065.7	c.916-5881T>C		intron_variant	Intron 8 of 12	1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.1037-5881T>C		intron_variant	Intron 8 of 11	1
SLC2A9	ENST00000506583.5	c.916-5881T>C		intron_variant	Intron 9 of 13	5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102915 AN: 151856 Hom.: 35070 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.678 AC: 102989 AN: 151974 Hom.: 35095 Cov.: 32 AF XY: 0.679 AC XY: 50433 AN XY: 74272

African (AFR) AF: 0.716 AC: 29667 AN: 41420

American (AMR) AF: 0.709 AC: 10844 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2034 AN: 3468

East Asian (EAS) AF: 0.778 AC: 4009 AN: 5156

South Asian (SAS) AF: 0.687 AC: 3313 AN: 4820

European-Finnish (FIN) AF: 0.674 AC: 7124 AN: 10566

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44018 AN: 67944

Other (OTH) AF: 0.662 AC: 1400 AN: 2114

Alfa AF: 0.660 Hom.: 22584

Bravo AF: 0.680

Asia WGS AF: 0.721 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.34
PhyloP100		-0.65
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: rs4697695; hg19: chr4-9915850;