rs10516195

Variant names:

• chr4-10000209-G-T
• rs10516195
• NM_020041.3:c.250-3268C>A

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-3268C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,202 control chromosomes in the GnomAD database, including 693 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 0.071 (693 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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.250-3268C>A		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.163-3268C>A		intron	N/A	NP_001001290.1	Q9NRM0-2
	SLC2A9-AS1	NR_183864.1		n.478G>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.250-3268C>A		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.163-3268C>A		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.284-3268C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10811 AN: 152084 Hom.: 693 Cov.: 33

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0712 AC: 10833 AN: 152202 Hom.: 693 Cov.: 33 AF XY: 0.0759 AC XY: 5649 AN XY: 74412

African (AFR) AF: 0.0904 AC: 3753 AN: 41526

American (AMR) AF: 0.0857 AC: 1310 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1961 AN: 5166

South Asian (SAS) AF: 0.112 AC: 541 AN: 4818

European-Finnish (FIN) AF: 0.0598 AC: 634 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0332 AC: 2256 AN: 68016

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0711 Hom.: 194

Bravo AF: 0.0756

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.58
PhyloP100		-1.0
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: rs10516195; hg19: chr4-10001833;