rs10516197

Variant names:

• chr4-10040476-C-T
• rs10516197
• ENST00000506583.5:c.-175-212G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506583.5(SLC2A9):​c.-175-212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,262 control chromosomes in the GnomAD database, including 1,353 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 0.10 (1353 hom., cov: 33)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 4 publications found

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:40636): (SLC2A9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_001001290.2	c.-387G>A		upstream_gene_variant			NP_001001290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-212G>A		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+14357G>A		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-15383C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15206 AN: 152090 Hom.: 1346 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0942

GnomAD4 exome AF: 0.0556 AC: 3 AN: 54 Hom.: 0 AF XY: 0.0750 AC XY: 3 AN XY: 40

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.0652 AC: 3 AN: 46

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.100 AC: 15235 AN: 152208 Hom.: 1353 Cov.: 33 AF XY: 0.106 AC XY: 7861 AN XY: 74414

African (AFR) AF: 0.131 AC: 5438 AN: 41548

American (AMR) AF: 0.183 AC: 2791 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2378 AN: 5178

South Asian (SAS) AF: 0.162 AC: 777 AN: 4810

European-Finnish (FIN) AF: 0.0726 AC: 769 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2549 AN: 68012

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0828 Hom.: 244

Bravo AF: 0.111

Asia WGS AF: 0.270 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.15
PromoterAI		0.0050	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10516197; hg19: chr4-10042100;