rs1005956

Variant names:

• chr12-39947283-T-C
• rs1005956
• NM_052885.4:c.1034+3974A>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.1034+3974A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,100 control chromosomes in the GnomAD database, including 8,728 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 0.33 (8728 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 11 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.1034+3974A>G		intron_variant	Intron 4 of 9	ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.1034+3974A>G		intron_variant	Intron 4 of 9	1	NM_052885.4	ENSP00000280871.4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49602 AN: 151982 Hom.: 8727 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.326 AC: 49628 AN: 152100 Hom.: 8728 Cov.: 32 AF XY: 0.325 AC XY: 24162 AN XY: 74358

African (AFR) AF: 0.209 AC: 8688 AN: 41504

American (AMR) AF: 0.273 AC: 4181 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3468

East Asian (EAS) AF: 0.177 AC: 919 AN: 5182

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4826

European-Finnish (FIN) AF: 0.446 AC: 4700 AN: 10544

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27561 AN: 67968

Other (OTH) AF: 0.314 AC: 664 AN: 2112

Alfa AF: 0.370 Hom.: 30945

Bravo AF: 0.300

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.72
PhyloP100		0.33
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: rs1005956; hg19: chr12-40341085;