4-10041226-C-G

Variant names:

• chr4-10041226-C-G
• rs7685958
• ENST00000506583.5:c.-175-962G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513129.1(SLC2A9):​c.-41+13607G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,244 control chromosomes in the GnomAD database, including 1,160 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 0.088 (1160 hom., cov: 34)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-962G>C		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+13607G>C		intron_variant	Intron 1 of 5	3		ENSP00000426800.1

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13400 AN: 152126 Hom.: 1157 Cov.: 34

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0882 AC: 13423 AN: 152244 Hom.: 1160 Cov.: 34 AF XY: 0.0940 AC XY: 7000 AN XY: 74438

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0367

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0125 Hom.: 5

Bravo AF: 0.0981

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7685958; hg19: chr4-10042850;