chr4-10023696-C-A

Variant names:

• chr4-10023696-C-A
• rs7696092
• ENST00000309065.7:c.63+2208G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309065.7(SLC2A9):​c.63+2208G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,146 control chromosomes in the GnomAD database, including 41,181 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 (41181 hom., cov: 33)
• Consequence: SLC2A9 ENST00000309065.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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.63+2208G>T		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.63+2208G>T		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.184+2208G>T		intron	N/A
	SLC2A9	ENST00000506583.5	TSL:5	c.63+2208G>T		intron	N/A	ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110730 AN: 152028 Hom.: 41148 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.728 AC: 110812 AN: 152146 Hom.: 41181 Cov.: 33 AF XY: 0.731 AC XY: 54390 AN XY: 74366

African (AFR) AF: 0.575 AC: 23842 AN: 41472

American (AMR) AF: 0.718 AC: 10992 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2433 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5061 AN: 5174

South Asian (SAS) AF: 0.811 AC: 3913 AN: 4826

European-Finnish (FIN) AF: 0.818 AC: 8665 AN: 10598

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53392 AN: 67982

Other (OTH) AF: 0.729 AC: 1540 AN: 2112

Alfa AF: 0.763 Hom.: 61882

Bravo AF: 0.714

Asia WGS AF: 0.882 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.095
DANN	Benign	0.25
PhyloP100		-2.0
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: rs7696092; hg19: chr4-10025320;