rs13106539

chr4-9796079-C-T

Variant summary

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

The XM_011513856.4(SLC2A9):c.1420-16014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,992 control chromosomes in the GnomAD database, including 22,178 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 0.52 (22178 hom., cov: 32)
• Consequence: SLC2A9 XM_011513856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

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 (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	XM_006713968.5	c.1601-16014G>A		intron_variant
SLC2A9	XM_011513856.4	c.1420-16014G>A		intron_variant
SLC2A9	XM_011513858.2	c.1333-16014G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000503803.5	n.386-16014G>A		intron_variant, non_coding_transcript_variant		3
SLC2A9	ENST00000508585.5	n.182-24710G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79471 AN: 151874 Hom.: 22164 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.523 AC: 79505 AN: 151992 Hom.: 22178 Cov.: 32 AF XY: 0.518 AC XY: 38475 AN XY: 74282

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.532

Alfa AF: 0.615 Hom.: 43886

Bravo AF: 0.506

Asia WGS AF: 0.334 AC: 1159 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	0.46
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13106539; hg19: chr4-9797703;