4-9777956-C-T

Variant summary

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

The XM_006713968.5(SLC2A9):c.*2018G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,856 control chromosomes in the GnomAD database, including 10,092 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 0.36 (10092 hom., cov: 32)
• Consequence: SLC2A9 XM_006713968.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	XM_006713968.5	c.*2018G>A		3_prime_UTR_variant	13/13
SLC2A9	XM_047415974.1	c.*1867G>A		3_prime_UTR_variant	12/12
SLC2A9	XM_047415977.1	c.*2018G>A		3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-6587G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54306 AN: 151738 Hom.: 10075 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.358 AC: 54355 AN: 151856 Hom.: 10092 Cov.: 32 AF XY: 0.362 AC XY: 26817 AN XY: 74178

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.361

Alfa AF: 0.331 Hom.: 1041

Bravo AF: 0.364

Asia WGS AF: 0.474 AC: 1650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10033951; hg19: chr4-9779580;