4-10040536-C-T

Position:

• chr4-10040536-C-T

Variant summary

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

The ENST00000513129.1(SLC2A9):​c.-41+14297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,010 control chromosomes in the GnomAD database, including 15,582 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 (15581 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.10040536C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-272G>A		intron_variant		5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+14297G>A		intron_variant		3		ENSP00000426800.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65216 AN: 151884 Hom.: 15576 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.443

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.429 AC: 65230 AN: 152002 Hom.: 15581 Cov.: 32 AF XY: 0.430 AC XY: 31936 AN XY: 74272

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.444

Alfa AF: 0.455 Hom.: 3266

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1767 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	0.69
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7679916; hg19: chr4-10042160;