rs4822442

Variant names:

• chr22-23879108-T-G
• rs4822442
• NM_001024939.4:c.694+1239T>G

Variant summary

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

The NM_001024939.4(SLC2A11):​c.694+1239T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,016 control chromosomes in the GnomAD database, including 45,398 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 0.77 (45398 hom., cov: 31)
• Consequence: SLC2A11 NM_001024939.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 11 publications found

Genes affected

SLC2A11 (HGNC:14239): (solute carrier family 2 member 11) This gene belongs to a family of proteins that mediate the transport of sugars across the cell membrane. The encoded protein transports glucose and fructose. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ENSG00000251357 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001024939.4. 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
	SLC2A11	NM_001024939.4	MANE Select	c.694+1239T>G		intron	N/A	NP_001020110.1
	SLC2A11	NM_001282864.2		c.706+1239T>G		intron	N/A	NP_001269793.1
	SLC2A11	NM_030807.5		c.706+1239T>G		intron	N/A	NP_110434.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A11	ENST00000316185.9	TSL:1 MANE Select	c.694+1239T>G		intron	N/A	ENSP00000326748.8
	SLC2A11	ENST00000398356.6	TSL:1	c.706+1239T>G		intron	N/A	ENSP00000381399.2
	SLC2A11	ENST00000345044.10	TSL:1	c.685+1239T>G		intron	N/A	ENSP00000342542.5

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116947 AN: 151898 Hom.: 45341 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.770 AC: 117062 AN: 152016 Hom.: 45398 Cov.: 31 AF XY: 0.774 AC XY: 57514 AN XY: 74294

African (AFR) AF: 0.869 AC: 36052 AN: 41472

American (AMR) AF: 0.807 AC: 12334 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3357 AN: 5176

South Asian (SAS) AF: 0.726 AC: 3490 AN: 4810

European-Finnish (FIN) AF: 0.782 AC: 8269 AN: 10572

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48551 AN: 67906

Other (OTH) AF: 0.754 AC: 1595 AN: 2116

Alfa AF: 0.730 Hom.: 74141

Bravo AF: 0.777

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		0.12
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: rs4822442; hg19: chr22-24221295;