4-10040938-A-T

Position:

• chr4-10040938-A-T

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-674T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,160 control chromosomes in the GnomAD database, including 45,643 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 0.77 (45643 hom., cov: 32)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-674T>A		intron_variant		5		ENSP00000422209	P2
SLC2A9	ENST00000513129.1	c.-41+13895T>A		intron_variant		3		ENSP00000426800

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117078 AN: 152042 Hom.: 45612 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.770 AC: 117153 AN: 152160 Hom.: 45643 Cov.: 32 AF XY: 0.764 AC XY: 56841 AN XY: 74400

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.760

Alfa AF: 0.793 Hom.: 5633

Bravo AF: 0.758

Asia WGS AF: 0.643 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.5
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: rs7349721; hg19: chr4-10042562;