ENST00000309065.7:c.-40-3533T>A

Variant names:

• chr4-10029539-A-T
• rs6856396
• ENST00000309065.7:c.-40-3533T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000309065.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_001001290.2		c.-40-3533T>A		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000309065.7	TSL:1	c.-40-3533T>A		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.82-3533T>A		intron	N/A
	SLC2A9	ENST00000506583.5	TSL:5	c.-40-3533T>A		intron	N/A	ENSP00000422209.1

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

African (AFR) AF: 0.813 AC: 33235 AN: 40868

American (AMR) AF: 0.804 AC: 12167 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2663 AN: 3458

East Asian (EAS) AF: 0.980 AC: 5066 AN: 5172

South Asian (SAS) AF: 0.840 AC: 4033 AN: 4802

European-Finnish (FIN) AF: 0.871 AC: 8277 AN: 9502

Middle Eastern (MID) AF: 0.831 AC: 236 AN: 284

European-Non Finnish (NFE) AF: 0.855 AC: 57776 AN: 67600

Other (OTH) AF: 0.833 AC: 1733 AN: 2080

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.14
PhyloP100		-0.093
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6856396; hg19: chr4-10031163;