chr4-10022679-T-C

Variant names:

• chr4-10022679-T-C
• rs12509955
• ENST00000309065.7:c.63+3225A>G

Variant summary

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

The NM_001001290.2(SLC2A9):​c.63+3225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,090 control chromosomes in the GnomAD database, including 41,708 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 0.73 (41708 hom., cov: 33)
• Consequence: SLC2A9 NM_001001290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001290.2. 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_001001290.2		c.63+3225A>G		intron	N/A	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000309065.7	TSL:1	c.63+3225A>G		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.184+3225A>G		intron	N/A
	SLC2A9	ENST00000506583.5	TSL:5	c.63+3225A>G		intron	N/A	ENSP00000422209.1	Q9NRM0-2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111562 AN: 151970 Hom.: 41676 Cov.: 33

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.734 AC: 111645 AN: 152090 Hom.: 41708 Cov.: 33 AF XY: 0.737 AC XY: 54779 AN XY: 74370

African (AFR) AF: 0.592 AC: 24524 AN: 41434

American (AMR) AF: 0.720 AC: 10996 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2434 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5061 AN: 5174

South Asian (SAS) AF: 0.810 AC: 3908 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8656 AN: 10582

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53545 AN: 68010

Other (OTH) AF: 0.732 AC: 1547 AN: 2112

Alfa AF: 0.765 Hom.: 107999

Bravo AF: 0.720

Asia WGS AF: 0.883 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.64
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: rs12509955; hg19: chr4-10024303;