NM_052885.4:c.926-9077C>T

Variant names:

• chr12-39960442-G-A
• rs11174478
• NM_052885.4:c.926-9077C>T

Variant summary

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

The NM_052885.4(SLC2A13):​c.926-9077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,098 control chromosomes in the GnomAD database, including 7,831 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 0.30 (7831 hom., cov: 33)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.926-9077C>T		intron_variant	Intron 3 of 9	ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.926-9077C>T		intron_variant	Intron 3 of 9	1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.926-9077C>T		intron_variant	Intron 3 of 3	1		ENSP00000370239.1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46276 AN: 151980 Hom.: 7830 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.304 AC: 46300 AN: 152098 Hom.: 7831 Cov.: 33 AF XY: 0.302 AC XY: 22473 AN XY: 74350

African (AFR) AF: 0.158 AC: 6552 AN: 41508

American (AMR) AF: 0.270 AC: 4120 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3470

East Asian (EAS) AF: 0.179 AC: 928 AN: 5172

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4148 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27022 AN: 67986

Other (OTH) AF: 0.301 AC: 634 AN: 2106

Alfa AF: 0.356 Hom.: 3644

Bravo AF: 0.281

Asia WGS AF: 0.288 AC: 1002 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	2.5
DANN	Benign	0.71
PhyloP100		-1.2
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: rs11174478; hg19: chr12-40354244;