rs10516197

chr4-10040476-C-T

Variant summary

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

The ENST00000506583.5(SLC2A9):c.-175-212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,262 control chromosomes in the GnomAD database, including 1,353 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 0.10 (1353 hom., cov: 33)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-212G>A		intron_variant		5		P2
SLC2A9	ENST00000513129.1	c.-41+14357G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15206 AN: 152090 Hom.: 1346 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0942

GnomAD4 exome AF: 0.0556 AC: 3 AN: 54 Hom.: 0 AF XY: 0.0750 AC XY: 3 AN XY: 40

Gnomad4 NFE exome AF: 0.0652

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.100 AC: 15235 AN: 152208 Hom.: 1353 Cov.: 33 AF XY: 0.106 AC XY: 7861 AN XY: 74414

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.0984

Alfa AF: 0.0595 Hom.: 100

Bravo AF: 0.111

Asia WGS AF: 0.270 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10516197; hg19: chr4-10042100;