rs12508991

chr4-10039480-C-T

Variant summary

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

The ENST00000309065.7(SLC2A9):c.-41+650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,148 control chromosomes in the GnomAD database, including 15,604 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 0.43 (15604 hom., cov: 33)
• Consequence: SLC2A9 ENST00000309065.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_001001290.2	c.-41+650G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000309065.7	c.-41+650G>A		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.81+650G>A		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.-41+650G>A		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65295 AN: 152030 Hom.: 15599 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.429 AC: 65309 AN: 152148 Hom.: 15604 Cov.: 33 AF XY: 0.430 AC XY: 31991 AN XY: 74370

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.444

Alfa AF: 0.515 Hom.: 8975

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.3
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12508991; hg19: chr4-10041104;