rs11174338

Variant names:

• chr12-39929839-G-T
• rs11174338
• NM_052885.4:c.1034+21418C>A

Variant summary

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

The ENST00000280871.9(SLC2A13):​c.1034+21418C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,138 control chromosomes in the GnomAD database, including 992 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 0.11 (992 hom., cov: 31)
• Consequence: SLC2A13 ENST00000280871.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000280871.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	NM_052885.4	MANE Select	c.1034+21418C>A		intron	N/A	NP_443117.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	ENST00000280871.9	TSL:1 MANE Select	c.1034+21418C>A		intron	N/A	ENSP00000280871.4

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16713 AN: 152018 Hom.: 991 Cov.: 31

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.110 AC: 16719 AN: 152138 Hom.: 992 Cov.: 31 AF XY: 0.107 AC XY: 7936 AN XY: 74388

African (AFR) AF: 0.0874 AC: 3631 AN: 41536

American (AMR) AF: 0.107 AC: 1632 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1003 AN: 5148

South Asian (SAS) AF: 0.0546 AC: 263 AN: 4816

European-Finnish (FIN) AF: 0.0677 AC: 718 AN: 10598

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8707 AN: 67964

Other (OTH) AF: 0.127 AC: 267 AN: 2110

Alfa AF: 0.117 Hom.: 556

Bravo AF: 0.114

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.72
PhyloP100		0.12
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: rs11174338; hg19: chr12-40323641;