rs10877840

Variant names:

• chr12-39959194-T-C
• rs10877840
• NM_052885.4:c.926-7829A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_052885.4(SLC2A13):​c.926-7829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,184 control chromosomes in the GnomAD database, including 3,254 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 0.19 (3254 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 13 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.926-7829A>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.926-7829A>G		intron_variant	Intron 3 of 9	1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.926-7829A>G		intron_variant	Intron 3 of 3	1		ENSP00000370239.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29557 AN: 152066 Hom.: 3253 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.194 AC: 29558 AN: 152184 Hom.: 3254 Cov.: 32 AF XY: 0.190 AC XY: 14163 AN XY: 74388

African (AFR) AF: 0.0998 AC: 4145 AN: 41550

American (AMR) AF: 0.182 AC: 2778 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1031 AN: 5172

South Asian (SAS) AF: 0.169 AC: 812 AN: 4810

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10594

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.255 AC: 17326 AN: 67986

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.237 Hom.: 8624

Bravo AF: 0.195

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.30
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: rs10877840; hg19: chr12-40352996;