rs10516195

chr4-10000209-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.250-3268C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,202 control chromosomes in the GnomAD database, including 693 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 0.071 (693 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.250-3268C>A		intron_variant		ENST00000264784.8
SLC2A9-AS1	NR_183861.1	n.412+1012G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.250-3268C>A		intron_variant		1	NM_020041.3	A2

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10811 AN: 152084 Hom.: 693 Cov.: 33

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0712 AC: 10833 AN: 152202 Hom.: 693 Cov.: 33 AF XY: 0.0759 AC XY: 5649 AN XY: 74412

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0598

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0620 Hom.: 119

Bravo AF: 0.0756

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.12
Dann	Benign	0.58

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: rs10516195; hg19: chr4-10001833;