rs10022499

chr4-10004913-C-Achr4-10004913-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020041.3(SLC2A9):c.250-7972G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,074 control chromosomes in the GnomAD database, including 40,192 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 0.72 (40192 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.250-7972G>T		intron_variant		ENST00000264784.8
SLC2A9-AS1	NR_183861.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.250-7972G>T		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109363 AN: 151956 Hom.: 40183 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.719 AC: 109408 AN: 152074 Hom.: 40192 Cov.: 33 AF XY: 0.716 AC XY: 53219 AN XY: 74336

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.726

Alfa AF: 0.775 Hom.: 19967

Bravo AF: 0.708

Asia WGS AF: 0.614 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.21
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs10022499; hg19: chr4-10006537;