chr12-40080345-C-T

Variant names:

• chr12-40080345-C-T
• rs4768212
• NM_052885.4:c.556+24908G>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.556+24908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,278 control chromosomes in the GnomAD database, including 68,676 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 0.95 (68676 hom., cov: 31)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 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.556+24908G>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.556+24908G>A		intron	N/A	ENSP00000280871.4
	SLC2A13	ENST00000380858.1	TSL:1	c.556+24908G>A		intron	N/A	ENSP00000370239.1
	ENSG00000294458	ENST00000723714.1		n.210-3525C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144437 AN: 152160 Hom.: 68619 Cov.: 31

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.949 AC: 144553 AN: 152278 Hom.: 68676 Cov.: 31 AF XY: 0.950 AC XY: 70759 AN XY: 74446

African (AFR) AF: 0.988 AC: 41039 AN: 41556

American (AMR) AF: 0.959 AC: 14674 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3239 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4926 AN: 5184

South Asian (SAS) AF: 0.882 AC: 4249 AN: 4820

European-Finnish (FIN) AF: 0.967 AC: 10252 AN: 10606

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63076 AN: 68016

Other (OTH) AF: 0.940 AC: 1988 AN: 2114

Alfa AF: 0.931 Hom.: 105830

Bravo AF: 0.951

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		-1.9
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: rs4768212; hg19: chr12-40474147;