rs13137343

Variant names:

• chr4-10041404-C-A
• rs13137343
• ENST00000506583.5:c.-175-1140G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-10041404-C-A
• chr4-10041404-C-G
• chr4-10041404-C-T

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-1140G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,060 control chromosomes in the GnomAD database, including 15,539 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 (15539 hom., cov: 33)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 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.-175-1140G>T		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+13429G>T		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-14455C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65108 AN: 151942 Hom.: 15535 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.428 AC: 65121 AN: 152060 Hom.: 15539 Cov.: 33 AF XY: 0.429 AC XY: 31902 AN XY: 74340

African (AFR) AF: 0.205 AC: 8512 AN: 41472

American (AMR) AF: 0.399 AC: 6103 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2204 AN: 5172

South Asian (SAS) AF: 0.586 AC: 2826 AN: 4822

European-Finnish (FIN) AF: 0.523 AC: 5531 AN: 10566

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36540 AN: 67970

Other (OTH) AF: 0.439 AC: 926 AN: 2108

Alfa AF: 0.458 Hom.: 2256

Bravo AF: 0.408

Asia WGS AF: 0.504 AC: 1749 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	3.0
DANN	Benign	0.53
PhyloP100		-0.017
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: rs13137343; hg19: chr4-10043028;