rs13148356

Positions:

• chr4-9815446-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.1419+19435C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,114 control chromosomes in the GnomAD database, including 21,243 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 0.51 (21243 hom., cov: 33)
• Consequence: SLC2A9 XM_011513856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	XM_006713968.5	c.1600+10974C>T		intron_variant			XP_006714031.1
SLC2A9	XM_011513856.4	c.1419+19435C>T		intron_variant			XP_011512158.1
SLC2A9	XM_011513858.2	c.1332+19435C>T		intron_variant			XP_011512160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000503280.5	n.420+10974C>T		intron_variant, non_coding_transcript_variant		4
SLC2A9	ENST00000503803.5	n.385+10974C>T		intron_variant, non_coding_transcript_variant		3
SLC2A9	ENST00000508585.5	n.181+10974C>T		intron_variant, non_coding_transcript_variant		3
SLC2A9	ENST00000512342.5	n.385+10974C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76820 AN: 151996 Hom.: 21238 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.505 AC: 76827 AN: 152114 Hom.: 21243 Cov.: 33 AF XY: 0.501 AC XY: 37261 AN XY: 74334

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.517

Alfa AF: 0.535 Hom.: 3578

Bravo AF: 0.485

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13148356; hg19: chr4-9817070;