4-9992591-C-T

Variant names:

• chr4-9992591-C-T
• rs6449213
• NM_020041.3:c.410+4190G>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.410+4190G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,242 control chromosomes in the GnomAD database, including 51,803 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.82 (51803 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.713
• Publications: 58 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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.410+4190G>A		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.323+4190G>A		intron	N/A	NP_001001290.1	Q9NRM0-2
	SLC2A9-AS1	NR_183861.1		n.23-664C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.410+4190G>A		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.323+4190G>A		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.444+4190G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125327 AN: 152124 Hom.: 51760 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.824 AC: 125424 AN: 152242 Hom.: 51803 Cov.: 33 AF XY: 0.824 AC XY: 61324 AN XY: 74434

African (AFR) AF: 0.856 AC: 35561 AN: 41540

American (AMR) AF: 0.767 AC: 11724 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5062 AN: 5178

South Asian (SAS) AF: 0.819 AC: 3953 AN: 4826

European-Finnish (FIN) AF: 0.829 AC: 8782 AN: 10590

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55070 AN: 68022

Other (OTH) AF: 0.819 AC: 1734 AN: 2116

Alfa AF: 0.813 Hom.: 162809

Bravo AF: 0.823

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Uric acid concentration, serum, quantitative trait locus 2 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.60
PhyloP100		-0.71
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: rs6449213; hg19: chr4-9994215;