rs11723970

Positions:

• chr4-9978838-T-C

Variant summary

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

The NM_020041.3(SLC2A9):​c.681+1754A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,172 control chromosomes in the GnomAD database, including 14,901 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 0.42 (14901 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.681+1754A>G		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+1754A>G		intron_variant		1	NM_020041.3	A2
SLC2A9	ENST00000309065.7	c.594+1754A>G		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.715+1754A>G		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.594+1754A>G		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64534 AN: 152054 Hom.: 14893 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.424 AC: 64541 AN: 152172 Hom.: 14901 Cov.: 33 AF XY: 0.425 AC XY: 31582 AN XY: 74390

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.443

Alfa AF: 0.478 Hom.: 7219

Bravo AF: 0.408

Asia WGS AF: 0.466 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.56

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: rs11723970; hg19: chr4-9980462;