4-10034715-A-G

Position:

• chr4-10034715-A-G

Variant summary

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

The NM_001001290.2(SLC2A9):​c.-41+5415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,084 control chromosomes in the GnomAD database, including 16,143 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 0.44 (16132 hom., cov: 32)
  • Exomes 𝑓: 0.57 (11 hom.)
• Consequence: SLC2A9 NM_001001290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_001001290.2	c.-41+5415T>C		intron_variant			NP_001001290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000309065.7	c.-41+5415T>C		intron_variant		1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.81+5415T>C		intron_variant		1
SLC2A9	ENST00000506583.5	c.-41+5415T>C		intron_variant		5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66457 AN: 151906 Hom.: 16123 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.449

GnomAD4 exome AF: 0.567 AC: 34 AN: 60 Hom.: 11 Cov.: 0 AF XY: 0.525 AC XY: 21 AN XY: 40

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.540

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.437 AC: 66477 AN: 152024 Hom.: 16132 Cov.: 32 AF XY: 0.439 AC XY: 32657 AN XY: 74310

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.449

Alfa AF: 0.518 Hom.: 10557

Bravo AF: 0.423

Asia WGS AF: 0.508 AC: 1764 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	0.96
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3733585; hg19: chr4-10036339;