chr4-10002376-A-G

Variant names:

• chr4-10002376-A-G
• rs7657096
• NM_020041.3:c.250-5435T>C

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-5435T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,224 control chromosomes in the GnomAD database, including 2,046 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 0.13 (2046 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.250-5435T>C		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.163-5435T>C		intron	N/A	NP_001001290.1	Q9NRM0-2
	SLC2A9-AS1	NR_183861.1		n.413-1752A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.250-5435T>C		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.163-5435T>C		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.284-5435T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19555 AN: 152106 Hom.: 2040 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.129 AC: 19603 AN: 152224 Hom.: 2046 Cov.: 33 AF XY: 0.133 AC XY: 9920 AN XY: 74432

African (AFR) AF: 0.229 AC: 9507 AN: 41506

American (AMR) AF: 0.115 AC: 1759 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2427 AN: 5172

South Asian (SAS) AF: 0.178 AC: 858 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 979 AN: 10610

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3487 AN: 68022

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.0860 Hom.: 1864

Bravo AF: 0.136

Asia WGS AF: 0.289 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.67
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: rs7657096; hg19: chr4-10004000;