4-10041404-C-A

Variant names:

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

Variant summary

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

The ENST00000513129.1(SLC2A9):​c.-41+13429G>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 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

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 (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

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.439

Alfa AF: 0.468 Hom.: 2234

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13137343; hg19: chr4-10043028;