4-9994768-A-T

Position:

• chr4-9994768-A-T

Variant summary

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

The NM_020041.3(SLC2A9):​c.410+2013T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 151,646 control chromosomes in the GnomAD database, including 51,923 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 0.83 (51923 hom., cov: 28)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+2013T>A		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+2013T>A		intron_variant		1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125213 AN: 151526 Hom.: 51880 Cov.: 28

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.826 AC: 125310 AN: 151646 Hom.: 51923 Cov.: 28 AF XY: 0.826 AC XY: 61193 AN XY: 74070

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.823

Alfa AF: 0.820 Hom.: 6378

Bravo AF: 0.826

Asia WGS AF: 0.900 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
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: rs4428284; hg19: chr4-9996392;