12-40080345-C-T

Position:

• chr12-40080345-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC112268095 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.556+24908G>A		intron_variant		ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.556+24908G>A		intron_variant		1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.556+24908G>A		intron_variant		1		ENSP00000370239.1

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

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.940

Alfa AF: 0.928 Hom.: 82120

Bravo AF: 0.951

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs4768212; hg19: chr12-40474147;