chr4-10048517-C-T

Variant names:

• chr4-10048517-C-T
• rs733175
• ENST00000506583.5:c.-176+6316G>A

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-176+6316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,920 control chromosomes in the GnomAD database, including 45,038 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 0.77 (45038 hom., cov: 30)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 21 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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.-176+6316G>A		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+6316G>A		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-7342C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116218 AN: 151802 Hom.: 45009 Cov.: 30

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.765 AC: 116292 AN: 151920 Hom.: 45038 Cov.: 30 AF XY: 0.759 AC XY: 56393 AN XY: 74258

African (AFR) AF: 0.766 AC: 31706 AN: 41400

American (AMR) AF: 0.630 AC: 9610 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2468 AN: 3466

East Asian (EAS) AF: 0.518 AC: 2667 AN: 5152

South Asian (SAS) AF: 0.678 AC: 3256 AN: 4804

European-Finnish (FIN) AF: 0.798 AC: 8442 AN: 10574

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55594 AN: 67958

Other (OTH) AF: 0.752 AC: 1584 AN: 2106

Alfa AF: 0.785 Hom.: 109368

Bravo AF: 0.753

Asia WGS AF: 0.641 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.56
PhyloP100		-0.94
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: rs733175; hg19: chr4-10050141;