4-10005039-G-T

Position:

• chr4-10005039-G-T

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-8098C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,062 control chromosomes in the GnomAD database, including 40,789 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 0.73 (40789 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.250-8098C>A		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.250-8098C>A		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110308 AN: 151942 Hom.: 40778 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.726 AC: 110356 AN: 152062 Hom.: 40789 Cov.: 32 AF XY: 0.722 AC XY: 53677 AN XY: 74336

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.730

Alfa AF: 0.777 Hom.: 20489

Bravo AF: 0.715

Asia WGS AF: 0.615 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.4
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10016075; hg19: chr4-10006663;