rs10939605

chr4-9894669-C-A

Variant summary

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

The NM_020041.3(SLC2A9):c.1114-3958G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,088 control chromosomes in the GnomAD database, including 5,078 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 0.25 (5078 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.1114-3958G>T		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.1114-3958G>T		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38544 AN: 151970 Hom.: 5072 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.254 AC: 38576 AN: 152088 Hom.: 5078 Cov.: 32 AF XY: 0.249 AC XY: 18524 AN XY: 74358

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.258

Alfa AF: 0.273 Hom.: 9768

Bravo AF: 0.258

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.4
Dann	Benign	0.83

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: rs10939605; hg19: chr4-9896293;