chr4-10041404-C-A

Position:

• chr4-10041404-C-A

Variant summary

Our verdict is Benign. Variant got -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

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-1140G>T		intron_variant		5		ENSP00000422209	P2
SLC2A9	ENST00000513129.1	c.-41+13429G>T		intron_variant		3		ENSP00000426800

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;