4-10002376-A-G

Position:

• chr4-10002376-A-G

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-5435T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,224 control chromosomes in the GnomAD database, including 2,046 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 0.13 (2046 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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]

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.250-5435T>C		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.250-5435T>C		intron_variant		1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19555 AN: 152106 Hom.: 2040 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.129 AC: 19603 AN: 152224 Hom.: 2046 Cov.: 33 AF XY: 0.133 AC XY: 9920 AN XY: 74432

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0799 Hom.: 354

Bravo AF: 0.136

Asia WGS AF: 0.289 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.67

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: rs7657096; hg19: chr4-10004000;