chr4-10042008-C-T

Position:

• chr4-10042008-C-T

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-1744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,992 control chromosomes in the GnomAD database, including 1,473 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 0.11 (1473 hom., cov: 33)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721

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 (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-1744G>A		intron_variant		5		P2
SLC2A9	ENST00000513129.1	c.-41+12825G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15927 AN: 151874 Hom.: 1464 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0374

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.105 AC: 15964 AN: 151992 Hom.: 1473 Cov.: 33 AF XY: 0.111 AC XY: 8245 AN XY: 74306

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0374

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0244 Hom.: 21

Bravo AF: 0.116

Asia WGS AF: 0.273 AC: 947 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	4.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36036984; hg19: chr4-10043632;