rs938554

chr4-9924068-C-Gchr4-9924068-C-T

Variant summary

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

The NM_020041.3(SLC2A9):c.815-3496G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,958 control chromosomes in the GnomAD database, including 40,028 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 0.72 (39998 hom., cov: 30)
  • Exomes 𝑓: 0.77 (30 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.815-3496G>C		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.815-3496G>C		intron_variant		1	NM_020041.3	A2
	ENST00000504249.1	n.430C>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108918 AN: 151736 Hom.: 39974 Cov.: 30

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.732

GnomAD4 exome AF: 0.775 AC: 79 AN: 102 Hom.: 30 Cov.: 0 AF XY: 0.762 AC XY: 61 AN XY: 80

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.718 AC: 108991 AN: 151856 Hom.: 39998 Cov.: 30 AF XY: 0.720 AC XY: 53458 AN XY: 74204

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.735

Alfa AF: 0.748 Hom.: 5357

Bravo AF: 0.700

Asia WGS AF: 0.847 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.83
Dann	Benign	0.56

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: rs938554; hg19: chr4-9925692;