4-9964756-A-G

Position:

• chr4-9964756-A-G

Variant summary

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

The NM_020041.3(SLC2A9):​c.681+15836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,134 control chromosomes in the GnomAD database, including 6,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.27 (6441 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.995

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.681+15836T>C		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+15836T>C		intron_variant		1	NM_020041.3	ENSP00000264784.3
SLC2A9	ENST00000309065.7	c.594+15836T>C		intron_variant		1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.715+15836T>C		intron_variant		1
SLC2A9	ENST00000506583.5	c.594+15836T>C		intron_variant		5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41739 AN: 152016 Hom.: 6429 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.275 AC: 41787 AN: 152134 Hom.: 6441 Cov.: 32 AF XY: 0.273 AC XY: 20336 AN XY: 74388

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.259

Alfa AF: 0.225 Hom.: 6680

Bravo AF: 0.291

Asia WGS AF: 0.160 AC: 556 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
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: rs7442295; hg19: chr4-9966380;