rs2896905
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_052885.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.427
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.354 AC: 53762AN: 151900Hom.: 9691 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
53762
AN:
151900
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.354 AC: 53796AN: 152018Hom.: 9692 Cov.: 32 AF XY: 0.348 AC XY: 25896AN XY: 74340 show subpopulations
GnomAD4 genome
AF:
AC:
53796
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
25896
AN XY:
74340
African (AFR)
AF:
AC:
14305
AN:
41438
American (AMR)
AF:
AC:
4116
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
1135
AN:
3470
East Asian (EAS)
AF:
AC:
1220
AN:
5168
South Asian (SAS)
AF:
AC:
1531
AN:
4816
European-Finnish (FIN)
AF:
AC:
4071
AN:
10550
Middle Eastern (MID)
AF:
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
AC:
26293
AN:
67976
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1028
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at