4-9994768-A-T

Variant names:

• chr4-9994768-A-T
• rs4428284
• NM_020041.3:c.410+2013T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+2013T>A		intron_variant	Intron 3 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+2013T>A		intron_variant	Intron 3 of 11	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

African (AFR) AF: 0.867 AC: 35814 AN: 41316

American (AMR) AF: 0.770 AC: 11719 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2553 AN: 3464

East Asian (EAS) AF: 0.977 AC: 5000 AN: 5116

South Asian (SAS) AF: 0.818 AC: 3927 AN: 4798

European-Finnish (FIN) AF: 0.826 AC: 8669 AN: 10490

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54871 AN: 67938

Other (OTH) AF: 0.823 AC: 1728 AN: 2100

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
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4428284; hg19: chr4-9996392;