rs6449179

chr4-9967493-G-Achr4-9967493-G-T

Variant summary

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

The NM_020041.3(SLC2A9):c.681+13099C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,670 control chromosomes in the GnomAD database, including 19,095 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 0.48 (19095 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.681+13099C>T		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+13099C>T		intron_variant		1	NM_020041.3	A2
SLC2A9	ENST00000309065.7	c.594+13099C>T		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.715+13099C>T		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.594+13099C>T		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73310 AN: 151560 Hom.: 19071 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.484 AC: 73374 AN: 151670 Hom.: 19095 Cov.: 33 AF XY: 0.477 AC XY: 35358 AN XY: 74120

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.465

Alfa AF: 0.296 Hom.: 654

Bravo AF: 0.498

Asia WGS AF: 0.251 AC: 858 AN: 3388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.81
Dann	Benign	0.12

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: rs6449179; hg19: chr4-9969117;