chr4-10042008-C-T

Variant names:

• chr4-10042008-C-T
• rs36036984
• ENST00000506583.5:c.-175-1744G>A

Variant summary

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

The ENST00000513129.1(SLC2A9):​c.-41+12825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,992 control chromosomes in the GnomAD database, including 1,473 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 0.11 (1473 hom., cov: 33)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513129.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000506583.5	TSL:5	c.-175-1744G>A		intron	N/A	ENSP00000422209.1	Q9NRM0-2
	SLC2A9	ENST00000513129.1	TSL:3	c.-41+12825G>A		intron	N/A	ENSP00000426800.1	D6REK5
	SLC2A9-AS1	ENST00000733256.1		n.319-13851C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15927 AN: 151874 Hom.: 1464 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0374

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.105 AC: 15964 AN: 151992 Hom.: 1473 Cov.: 33 AF XY: 0.111 AC XY: 8245 AN XY: 74306

African (AFR) AF: 0.147 AC: 6109 AN: 41438

American (AMR) AF: 0.185 AC: 2827 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0704 AC: 244 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5174

South Asian (SAS) AF: 0.162 AC: 778 AN: 4814

European-Finnish (FIN) AF: 0.0736 AC: 777 AN: 10556

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0374 AC: 2545 AN: 67962

Other (OTH) AF: 0.103 AC: 216 AN: 2106

Alfa AF: 0.0813 Hom.: 180

Bravo AF: 0.116

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		0.72
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: rs36036984; hg19: chr4-10043632;