4-9983972-G-A

Position:

• chr4-9983972-G-A

Variant summary

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

The NM_020041.3(SLC2A9):​c.535+1697C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,130 control chromosomes in the GnomAD database, including 49,355 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 0.80 (49355 hom., cov: 31)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.535+1697C>T		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.535+1697C>T		intron_variant		1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121903 AN: 152012 Hom.: 49301 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.802 AC: 122013 AN: 152130 Hom.: 49355 Cov.: 31 AF XY: 0.800 AC XY: 59495 AN XY: 74360

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.798

Alfa AF: 0.771 Hom.: 12492

Bravo AF: 0.797

Asia WGS AF: 0.858 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.72

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: rs7680126; hg19: chr4-9985596;