4-10022679-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 ENST00000309065.7(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 ENST00000309065.7 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_001001290.2	c.63+3225A>G		intron_variant	Intron 2 of 12		NP_001001290.1
SLC2A9	XM_011513858.2	c.63+3225A>G		intron_variant	Intron 2 of 13		XP_011512160.1
SLC2A9	XM_047415973.1	c.63+3225A>G		intron_variant	Intron 2 of 13		XP_047271929.1
SLC2A9	XM_047415975.1	c.63+3225A>G		intron_variant	Intron 2 of 12		XP_047271931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000309065.7	c.63+3225A>G		intron_variant	Intron 2 of 12	1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.184+3225A>G		intron_variant	Intron 2 of 11	1
SLC2A9	ENST00000506583.5	c.63+3225A>G		intron_variant	Intron 3 of 13	5		ENSP00000422209.1

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 v4.3

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;