rs11723439

Positions:

• chr4-9950195-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.682-8150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,168 control chromosomes in the GnomAD database, including 2,336 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 0.17 (2336 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.682-8150G>A		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.682-8150G>A		intron_variant		1	NM_020041.3	ENSP00000264784	A2
SLC2A9	ENST00000309065.7	c.595-8150G>A		intron_variant		1		ENSP00000311383	P2
SLC2A9	ENST00000505104.5	n.716-8150G>A		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.595-8150G>A		intron_variant		5		ENSP00000422209	P2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25168 AN: 152050 Hom.: 2333 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.165 AC: 25178 AN: 152168 Hom.: 2336 Cov.: 32 AF XY: 0.166 AC XY: 12345 AN XY: 74392

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.170

Alfa AF: 0.181 Hom.: 643

Bravo AF: 0.164

Asia WGS AF: 0.0950 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.34

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: rs11723439; hg19: chr4-9951819;