4-10029539-A-T

Position:

• chr4-10029539-A-T

Variant summary

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

The ENST00000309065.7(SLC2A9):​c.-40-3533T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 149,808 control chromosomes in the GnomAD database, including 52,994 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 0.84 (52994 hom., cov: 30)
• Consequence: SLC2A9 ENST00000309065.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_001001290.2	c.-40-3533T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000309065.7	c.-40-3533T>A		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.82-3533T>A		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.-40-3533T>A		intron_variant		5		P2
SLC2A9	ENST00000513129.1	c.-40-3533T>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.841 AC: 125917 AN: 149718 Hom.: 52967 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.841 AC: 125983 AN: 149808 Hom.: 52994 Cov.: 30 AF XY: 0.842 AC XY: 61607 AN XY: 73182

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.833

Alfa AF: 0.844 Hom.: 6332

Bravo AF: 0.837

Asia WGS AF: 0.904 AC: 3136 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6856396; hg19: chr4-10031163;