12-40084850-G-T

Variant names:

• chr12-40084850-G-T
• rs2708453
• NM_052885.4:c.556+20403C>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+20403C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,944 control chromosomes in the GnomAD database, including 1,220 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 0.12 (1220 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 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+20403C>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+20403C>A		intron	N/A	ENSP00000280871.4
	SLC2A13	ENST00000380858.1	TSL:1	c.556+20403C>A		intron	N/A	ENSP00000370239.1
	ENSG00000294458	ENST00000723714.1		n.307-202G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18389 AN: 151824 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.121 AC: 18406 AN: 151944 Hom.: 1220 Cov.: 32 AF XY: 0.118 AC XY: 8786 AN XY: 74300

African (AFR) AF: 0.0795 AC: 3297 AN: 41474

American (AMR) AF: 0.100 AC: 1532 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3468

East Asian (EAS) AF: 0.0540 AC: 279 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1093 AN: 4802

European-Finnish (FIN) AF: 0.0888 AC: 939 AN: 10578

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10336 AN: 67892

Other (OTH) AF: 0.130 AC: 273 AN: 2106

Alfa AF: 0.144 Hom.: 7056

Bravo AF: 0.117

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.32
PhyloP100		-1.1
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: rs2708453; hg19: chr12-40478652;