4-10016529-C-A

Position:

• chr4-10016529-C-A

Variant summary

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

The NM_020041.3(SLC2A9):​c.249+2446G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,700 control chromosomes in the GnomAD database, including 23,742 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 0.55 (23742 hom., cov: 30)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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]

LOC124900664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.249+2446G>T		intron_variant		ENST00000264784.8	NP_064425.2
LOC124900664	XR_007058024.1	n.7265C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.249+2446G>T		intron_variant		1	NM_020041.3	ENSP00000264784	A2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83155 AN: 151582 Hom.: 23711 Cov.: 30

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.549 AC: 83231 AN: 151700 Hom.: 23742 Cov.: 30 AF XY: 0.555 AC XY: 41145 AN XY: 74098

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.557

Alfa AF: 0.569 Hom.: 12447

Bravo AF: 0.541

Asia WGS AF: 0.788 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.49

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: rs6827754; hg19: chr4-10018153;