4-10054752-T-C

Position:

• chr4-10054752-T-C

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-176+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,152 control chromosomes in the GnomAD database, including 41,580 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 0.73 (41576 hom., cov: 33)
  • Exomes 𝑓: 0.60 (4 hom.)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-176+81A>G		intron_variant		5		P2
SLC2A9	ENST00000513129.1	c.-41+81A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111276 AN: 152014 Hom.: 41545 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.732

GnomAD4 exome AF: 0.600 AC: 12 AN: 20 Hom.: 4 AF XY: 0.750 AC XY: 12 AN XY: 16

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.643

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.732 AC: 111358 AN: 152132 Hom.: 41576 Cov.: 33 AF XY: 0.735 AC XY: 54675 AN XY: 74362

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.735

Alfa AF: 0.775 Hom.: 49406

Bravo AF: 0.717

Asia WGS AF: 0.882 AC: 3066 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	0.92
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7671266; hg19: chr4-10056376;