rs7696092

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-10023696-C-A
• chr4-10023696-C-G
• chr4-10023696-C-T

Variant summary

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

The NM_001001290.2(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 NM_001001290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_001001290.2	c.63+2208G>T		intron_variant	Intron 2 of 12		NP_001001290.1
SLC2A9	XM_011513858.2	c.63+2208G>T		intron_variant	Intron 2 of 13		XP_011512160.1
SLC2A9	XM_047415973.1	c.63+2208G>T		intron_variant	Intron 2 of 13		XP_047271929.1
SLC2A9	XM_047415975.1	c.63+2208G>T		intron_variant	Intron 2 of 12		XP_047271931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000309065.7	c.63+2208G>T		intron_variant	Intron 2 of 12	1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.184+2208G>T		intron_variant	Intron 2 of 11	1
SLC2A9	ENST00000506583.5	c.63+2208G>T		intron_variant	Intron 3 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.63+2208G>T		intron_variant	Intron 2 of 5	3		ENSP00000426800.1

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

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.729

Alfa AF: 0.749 Hom.: 7638

Bravo AF: 0.714

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	-0.97
CADD	Benign	0.095
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7696092; hg19: chr4-10025320;