rs12499857

chr4-9993752-G-A

Variant summary

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

The NM_020041.3(SLC2A9):c.410+3029C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,678 control chromosomes in the GnomAD database, including 17,691 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 0.46 (17691 hom., cov: 30)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

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]

SLC2A9-AS1 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.410+3029C>T		intron_variant		ENST00000264784.8
SLC2A9-AS1	NR_183861.1	n.142+378G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+3029C>T		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69690 AN: 151560 Hom.: 17683 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.460 AC: 69710 AN: 151678 Hom.: 17691 Cov.: 30 AF XY: 0.463 AC XY: 34313 AN XY: 74108

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.480

Alfa AF: 0.535 Hom.: 10568

Bravo AF: 0.450

Asia WGS AF: 0.515 AC: 1788 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	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12499857; hg19: chr4-9995376;