rs4822442

chr22-23879108-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A11	NM_001024939.4	c.694+1239T>G		intron_variant		ENST00000316185.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A11	ENST00000316185.9	c.694+1239T>G		intron_variant		1	NM_001024939.4

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

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.754

Alfa AF: 0.726 Hom.: 52954

Bravo AF: 0.777

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.4
Dann	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs4822442; hg19: chr22-24221295;