rs11202059
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145868.2(ANXA11):c.-58+10256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,022 control chromosomes in the GnomAD database, including 1,916 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 0.14 ( 1916 hom., cov: 32)
Consequence
ANXA11
NM_145868.2 intron
NM_145868.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.48
Publications
3 publications found
Genes affected
ANXA11 (HGNC:535): (annexin A11) This gene encodes a member of the annexin family, a group of calcium-dependent phospholipid-binding proteins. Annexins have unique N-terminal domains and conserved C-terminal domains, which contain calcium-dependent phospholipid-binding sites. The encoded protein is a 56-kD antigen recognized by sera from patients with various autoimmune diseases. Several transcript variants encoding two different isoforms have been identified. [provided by RefSeq, Dec 2015]
ANXA11 Gene-Disease associations (from GenCC):
- amyotrophic lateral sclerosis type 23Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- inclusion body myopathy and brain white matter abnormalitiesInheritance: AD Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- amyotrophic lateral sclerosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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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=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.142 AC: 21596AN: 151904Hom.: 1908 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21596
AN:
151904
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: 0.142 AC: 21629AN: 152022Hom.: 1916 Cov.: 32 AF XY: 0.145 AC XY: 10784AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
21629
AN:
152022
Hom.:
Cov.:
32
AF XY:
AC XY:
10784
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
9850
AN:
41446
American (AMR)
AF:
AC:
1234
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
287
AN:
3470
East Asian (EAS)
AF:
AC:
1090
AN:
5150
South Asian (SAS)
AF:
AC:
1145
AN:
4810
European-Finnish (FIN)
AF:
AC:
1514
AN:
10584
Middle Eastern (MID)
AF:
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6158
AN:
67972
Other (OTH)
AF:
AC:
273
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
898
1795
2693
3590
4488
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
791
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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