rs7669607

Variant names:

• chr4-9996177-T-C
• rs7669607
• NM_020041.3:c.410+604A>G

Variant summary

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

The NM_020041.3(SLC2A9):​c.410+604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,198 control chromosomes in the GnomAD database, including 48,907 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 0.80 (48907 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+604A>G		intron_variant	Intron 3 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+604A>G		intron_variant	Intron 3 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121756 AN: 152080 Hom.: 48873 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.801 AC: 121845 AN: 152198 Hom.: 48907 Cov.: 32 AF XY: 0.800 AC XY: 59563 AN XY: 74420

African (AFR) AF: 0.823 AC: 34187 AN: 41518

American (AMR) AF: 0.751 AC: 11493 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2512 AN: 3462

East Asian (EAS) AF: 0.967 AC: 5012 AN: 5184

South Asian (SAS) AF: 0.792 AC: 3818 AN: 4822

European-Finnish (FIN) AF: 0.795 AC: 8420 AN: 10594

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53739 AN: 68002

Other (OTH) AF: 0.798 AC: 1688 AN: 2114

Alfa AF: 0.795 Hom.: 79267

Bravo AF: 0.800

Asia WGS AF: 0.884 AC: 3070 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.43
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7669607; hg19: chr4-9997801; COSMIC: COSV53316567;