rs10939515

chr4-9771672-G-A

Variant summary

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

The XM_011513856.4(SLC2A9):c.1619-303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,228 control chromosomes in the GnomAD database, including 3,116 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 0.19 (3116 hom., cov: 34)
• Consequence: SLC2A9 XM_011513856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	XM_011513856.4	c.1619-303C>T		intron_variant
SLC2A9	XM_011513858.2	c.1532-303C>T		intron_variant
SLC2A9	XM_011513864.3	c.1211-303C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-303C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29639 AN: 152110 Hom.: 3110 Cov.: 34

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.195 AC: 29660 AN: 152228 Hom.: 3116 Cov.: 34 AF XY: 0.196 AC XY: 14586 AN XY: 74438

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.186

Alfa AF: 0.184 Hom.: 451

Bravo AF: 0.200

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.21
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10939515; hg19: chr4-9773296;