12-40034759-G-T

Variant names:

• chr12-40034759-G-T
• rs1994090
• NM_052885.4:c.717-6250C>A

Variant summary

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

The NM_052885.4(SLC2A13):​c.717-6250C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,148 control chromosomes in the GnomAD database, including 53,538 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 0.84 (53538 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 38 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052885.4. 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
	SLC2A13	NM_052885.4	MANE Select	c.717-6250C>A		intron	N/A	NP_443117.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	ENST00000280871.9	TSL:1 MANE Select	c.717-6250C>A		intron	N/A	ENSP00000280871.4
	SLC2A13	ENST00000380858.1	TSL:1	c.717-6250C>A		intron	N/A	ENSP00000370239.1

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127221 AN: 152030 Hom.: 53483 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.837 AC: 127334 AN: 152148 Hom.: 53538 Cov.: 32 AF XY: 0.840 AC XY: 62489 AN XY: 74380

African (AFR) AF: 0.916 AC: 38047 AN: 41518

American (AMR) AF: 0.871 AC: 13312 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2740 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4885 AN: 5180

South Asian (SAS) AF: 0.741 AC: 3571 AN: 4820

European-Finnish (FIN) AF: 0.823 AC: 8705 AN: 10582

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53362 AN: 67974

Other (OTH) AF: 0.838 AC: 1768 AN: 2110

Alfa AF: 0.803 Hom.: 198822

Bravo AF: 0.845

Asia WGS AF: 0.853 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		0.13
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: rs1994090; hg19: chr12-40428561;