rs10018204

Variant names:

• chr4-9962946-C-T
• rs10018204
• NM_020041.3:c.681+17646G>A

Variant summary

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

The NM_020041.3(SLC2A9):​c.681+17646G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,016 control chromosomes in the GnomAD database, including 19,082 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 0.48 (19082 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.681+17646G>A		intron_variant	Intron 5 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+17646G>A		intron_variant	Intron 5 of 11	1	NM_020041.3	ENSP00000264784.3
SLC2A9	ENST00000309065.7	c.594+17646G>A		intron_variant	Intron 6 of 12	1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.715+17646G>A		intron_variant	Intron 6 of 11	1
SLC2A9	ENST00000506583.5	c.594+17646G>A		intron_variant	Intron 7 of 13	5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73322 AN: 151898 Hom.: 19059 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.483 AC: 73387 AN: 152016 Hom.: 19082 Cov.: 32 AF XY: 0.476 AC XY: 35370 AN XY: 74302

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.463

Alfa AF: 0.487 Hom.: 3725

Bravo AF: 0.497

Asia WGS AF: 0.253 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.71

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: rs10018204; hg19: chr4-9964570;