rs2896905

Variant names:

• chr12-40099614-G-A
• rs2896905
• NM_052885.4:c.556+5639C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-40099614-G-A
• chr12-40099614-G-C

Variant summary

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

The NM_052885.4(SLC2A13):​c.556+5639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,018 control chromosomes in the GnomAD database, including 9,692 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 0.35 (9692 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 22 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052885.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	NM_052885.4	MANE Select	c.556+5639C>T		intron	N/A	NP_443117.3	Q96QE2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	ENST00000280871.9	TSL:1 MANE Select	c.556+5639C>T		intron	N/A	ENSP00000280871.4	Q96QE2
	SLC2A13	ENST00000380858.1	TSL:1	c.556+5639C>T		intron	N/A	ENSP00000370239.1	E9PE47
	SLC2A13	ENST00000957640.1		c.556+5639C>T		intron	N/A	ENSP00000627699.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53762 AN: 151900 Hom.: 9691 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.354 AC: 53796 AN: 152018 Hom.: 9692 Cov.: 32 AF XY: 0.348 AC XY: 25896 AN XY: 74340

African (AFR) AF: 0.345 AC: 14305 AN: 41438

American (AMR) AF: 0.269 AC: 4116 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4816

European-Finnish (FIN) AF: 0.386 AC: 4071 AN: 10550

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

European-Non Finnish (NFE) AF: 0.387 AC: 26293 AN: 67976

Other (OTH) AF: 0.352 AC: 741 AN: 2108

Alfa AF: 0.366 Hom.: 16157

Bravo AF: 0.347

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.8
DANN	Benign	0.84
PhyloP100		0.43
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: rs2896905; hg19: chr12-40493416;