chr4-9995488-C-A

Variant names:

• chr4-9995488-C-A
• rs4529048
• NM_020041.3:c.410+1293G>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+1293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,084 control chromosomes in the GnomAD database, including 38,876 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 0.71 (38876 hom., cov: 31)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+1293G>T		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+1293G>T		intron_variant	Intron 3 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108418 AN: 151966 Hom.: 38860 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.713 AC: 108477 AN: 152084 Hom.: 38876 Cov.: 31 AF XY: 0.709 AC XY: 52703 AN XY: 74340

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.717

Alfa AF: 0.685 Hom.: 6506

Bravo AF: 0.707

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs4529048; hg19: chr4-9997112;