chr5-151110636-A-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001155.5(ANXA6):c.1581T>G(p.Ala527Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000044 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ANXA6
NM_001155.5 synonymous
NM_001155.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.53
Publications
0 publications found
Genes affected
ANXA6 (HGNC:544): (annexin A6) Annexin VI belongs to a family of calcium-dependent membrane and phospholipid binding proteins. Several members of the annexin family have been implicated in membrane-related events along exocytotic and endocytotic pathways. The annexin VI gene is approximately 60 kbp long and contains 26 exons. It encodes a protein of about 68 kDa that consists of eight 68-amino acid repeats separated by linking sequences of variable lengths. It is highly similar to human annexins I and II sequences, each of which contain four such repeats. Annexin VI has been implicated in mediating the endosome aggregation and vesicle fusion in secreting epithelia during exocytosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 5-151110636-A-C is Benign according to our data. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-151110636-A-C is described in CliVar as Likely_benign. Clinvar id is 737896.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.53 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ANXA6 | NM_001155.5 | c.1581T>G | p.Ala527Ala | synonymous_variant | Exon 21 of 26 | ENST00000354546.10 | NP_001146.2 | |
| ANXA6 | NM_001193544.2 | c.1485T>G | p.Ala495Ala | synonymous_variant | Exon 20 of 25 | NP_001180473.1 | ||
| ANXA6 | NM_001363114.2 | c.1573-790T>G | intron_variant | Intron 20 of 24 | NP_001350043.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000439 AC: 64AN: 1457164Hom.: 0 Cov.: 30 AF XY: 0.0000386 AC XY: 28AN XY: 724962 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
64
AN:
1457164
Hom.:
Cov.:
30
AF XY:
AC XY:
28
AN XY:
724962
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
33376
American (AMR)
AF:
AC:
1
AN:
44642
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26040
East Asian (EAS)
AF:
AC:
1
AN:
39522
South Asian (SAS)
AF:
AC:
3
AN:
86172
European-Finnish (FIN)
AF:
AC:
1
AN:
53158
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
52
AN:
1108334
Other (OTH)
AF:
AC:
3
AN:
60164
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.255
Heterozygous variant carriers
0
7
15
22
30
37
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 20, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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