4-9992591-C-T

Variant summary

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

The NM_020041.3(SLC2A9):c.410+4190G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,242 control chromosomes in the GnomAD database, including 51,803 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.82 (51803 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.713

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.410+4190G>A		intron_variant		ENST00000264784.8
SLC2A9-AS1	NR_183861.1	n.23-664C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+4190G>A		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125327 AN: 152124 Hom.: 51760 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.824 AC: 125424 AN: 152242 Hom.: 51803 Cov.: 33 AF XY: 0.824 AC XY: 61324 AN XY: 74434

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.819

Alfa AF: 0.808 Hom.: 68887

Bravo AF: 0.823

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Uric acid concentration, serum, quantitative trait locus 2 Other:1

association, no assertion criteria provided

literature only

OMIM

Apr 01, 2008

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.80
Dann	Benign	0.60

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: rs6449213; hg19: chr4-9994215;