NM_052885.4:c.925+6509A>G

Variant names:

• chr12-40021792-T-C
• rs520138
• NM_052885.4:c.925+6509A>G

Variant summary

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

The NM_052885.4(SLC2A13):​c.925+6509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,038 control chromosomes in the GnomAD database, including 33,899 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 0.66 (33899 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.925+6509A>G		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.925+6509A>G		intron_variant	Intron 3 of 9	1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.925+6509A>G		intron_variant	Intron 3 of 3	1		ENSP00000370239.1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100904 AN: 151920 Hom.: 33844 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.664 AC: 101018 AN: 152038 Hom.: 33899 Cov.: 32 AF XY: 0.664 AC XY: 49334 AN XY: 74334

African (AFR) AF: 0.731 AC: 30357 AN: 41502

American (AMR) AF: 0.680 AC: 10382 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1978 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2358 AN: 5166

South Asian (SAS) AF: 0.498 AC: 2398 AN: 4820

European-Finnish (FIN) AF: 0.697 AC: 7365 AN: 10562

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44018 AN: 67928

Other (OTH) AF: 0.670 AC: 1417 AN: 2114

Alfa AF: 0.641 Hom.: 15069

Bravo AF: 0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.72
PhyloP100		0.72
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: rs520138; hg19: chr12-40415594;