rs2896905

Positions:

• chr12-40099614-G-A
• chr12-40099614-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052885.4(SLC2A13):​c.556+5639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,018 control chromosomes in the GnomAD database, including 9,692 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 0.35 (9692 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A13	NM_052885.4	c.556+5639C>T		intron_variant		ENST00000280871.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A13	ENST00000280871.9	c.556+5639C>T		intron_variant		1	NM_052885.4	P1
SLC2A13	ENST00000380858.1	c.556+5639C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53762 AN: 151900 Hom.: 9691 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.354 AC: 53796 AN: 152018 Hom.: 9692 Cov.: 32 AF XY: 0.348 AC XY: 25896 AN XY: 74340

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.352

Alfa AF: 0.364 Hom.: 13356

Bravo AF: 0.347

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.8
DANN	Benign	0.84

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: rs2896905; hg19: chr12-40493416;