12-40049090-A-G

Variant names:

• chr12-40049090-A-G
• rs11564162
• NM_052885.4:c.557-880T>C

Variant summary

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

The NM_052885.4(SLC2A13):​c.557-880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,002 control chromosomes in the GnomAD database, including 2,170 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 0.15 (2170 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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.557-880T>C		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.557-880T>C		intron	N/A	ENSP00000280871.4
	SLC2A13	ENST00000380858.1	TSL:1	c.557-880T>C		intron	N/A	ENSP00000370239.1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22666 AN: 151884 Hom.: 2171 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.149 AC: 22672 AN: 152002 Hom.: 2170 Cov.: 32 AF XY: 0.149 AC XY: 11067 AN XY: 74280

African (AFR) AF: 0.0434 AC: 1800 AN: 41506

American (AMR) AF: 0.111 AC: 1693 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3468

East Asian (EAS) AF: 0.0943 AC: 488 AN: 5174

South Asian (SAS) AF: 0.141 AC: 681 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2811 AN: 10532

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13870 AN: 67918

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.193 Hom.: 3479

Bravo AF: 0.135

Asia WGS AF: 0.146 AC: 505 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.89
PhyloP100		0.41
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: rs11564162; hg19: chr12-40442892;