NM_052885.4:c.557-23930A>G

Variant names:

• chr12-40072140-T-C
• rs7304279
• NM_052885.4:c.557-23930A>G

Variant summary

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

The NM_052885.4(SLC2A13):​c.557-23930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,102 control chromosomes in the GnomAD database, including 57,285 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 0.87 (57285 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 11 publications found

Genes affected

SLC2A13 (HGNC:15956): (solute carrier family 2 member 13) Enables ATPase binding activity; myo-inositol:proton symporter activity; and protease binding activity. Involved in myo-inositol transport and positive regulation of amyloid-beta formation. Is integral component of plasma membrane. Part of cell body; cell periphery; and cell projection. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000294458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.557-23930A>G		intron_variant	Intron 1 of 9	ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.557-23930A>G		intron_variant	Intron 1 of 9	1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.557-23930A>G		intron_variant	Intron 1 of 3	1		ENSP00000370239.1
ENSG00000294458	ENST00000723714.1	n.-237T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131837 AN: 151984 Hom.: 57241 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.867 AC: 131937 AN: 152102 Hom.: 57285 Cov.: 32 AF XY: 0.870 AC XY: 64699 AN XY: 74346

African (AFR) AF: 0.885 AC: 36762 AN: 41530

American (AMR) AF: 0.895 AC: 13670 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4907 AN: 5186

South Asian (SAS) AF: 0.771 AC: 3716 AN: 4818

European-Finnish (FIN) AF: 0.911 AC: 9654 AN: 10592

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57438 AN: 67918

Other (OTH) AF: 0.861 AC: 1818 AN: 2112

Alfa AF: 0.850 Hom.: 8552

Bravo AF: 0.871

Asia WGS AF: 0.858 AC: 2977 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		-2.0
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: rs7304279; hg19: chr12-40465942;