rs2896905

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.427
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A13NM_052885.4 linkc.556+5639C>T intron_variant Intron 1 of 9 ENST00000280871.9 NP_443117.3 Q96QE2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A13ENST00000280871.9 linkc.556+5639C>T intron_variant Intron 1 of 9 1 NM_052885.4 ENSP00000280871.4 Q96QE2
SLC2A13ENST00000380858.1 linkc.556+5639C>T intron_variant Intron 1 of 3 1 ENSP00000370239.1 E9PE47

Frequencies

GnomAD3 genomes
AF:
0.354
AC:
53762
AN:
151900
Hom.:
9691
Cov.:
32
show subpopulations
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
show subpopulations
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
Heterozygous variant carriers
0
1772
3545
5317
7090
8862
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
540
1080
1620
2160
2700
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.8
DANN
Benign
0.84
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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2896905; hg19: chr12-40493416; API