ENST00000506583.5:c.-175-1998T>G

Variant names:

• chr4-10042262-A-C
• rs62293415
• ENST00000506583.5:c.-175-1998T>G

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-1998T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,064 control chromosomes in the GnomAD database, including 15,634 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 0.43 (15634 hom., cov: 33)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.569 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.-175-1998T>G		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+12571T>G		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-13597A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65438 AN: 151948 Hom.: 15629 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.430 AC: 65452 AN: 152064 Hom.: 15634 Cov.: 33 AF XY: 0.431 AC XY: 32060 AN XY: 74356

African (AFR) AF: 0.211 AC: 8765 AN: 41486

American (AMR) AF: 0.403 AC: 6157 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2200 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4822

European-Finnish (FIN) AF: 0.522 AC: 5514 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36563 AN: 67960

Other (OTH) AF: 0.448 AC: 941 AN: 2102

Alfa AF: 0.469 Hom.: 2237

Bravo AF: 0.410

Asia WGS AF: 0.509 AC: 1766 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	5.9
DANN	Benign	0.85
PhyloP100		0.13
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: rs62293415; hg19: chr4-10043886;