rs17187075

Variant names:

• chr4-9988704-G-C
• rs17187075
• NM_020041.3:c.411-2911C>G

Variant summary

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

The NM_020041.3(SLC2A9):​c.411-2911C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,062 control chromosomes in the GnomAD database, including 17,028 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 0.46 (17028 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 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 (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.411-2911C>G		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.324-2911C>G		intron	N/A	NP_001001290.1	Q9NRM0-2
	SLC2A9-AS1	NR_183861.1		n.22+560G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.411-2911C>G		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.324-2911C>G		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.445-2911C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69219 AN: 151944 Hom.: 17012 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.455 AC: 69261 AN: 152062 Hom.: 17028 Cov.: 32 AF XY: 0.457 AC XY: 33996 AN XY: 74324

African (AFR) AF: 0.255 AC: 10598 AN: 41488

American (AMR) AF: 0.496 AC: 7582 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2153 AN: 5166

South Asian (SAS) AF: 0.585 AC: 2822 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5550 AN: 10560

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37058 AN: 67960

Other (OTH) AF: 0.464 AC: 979 AN: 2112

Alfa AF: 0.487 Hom.: 2368

Bravo AF: 0.443

Asia WGS AF: 0.512 AC: 1777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.68
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17187075; hg19: chr4-9990328;