rs5796316
Your query was ambiguous. Multiple possible variants found:
- chr12-8604926-CAAAAAAAAA-C
- chr12-8604926-CAAAAAAAAA-CA
- chr12-8604926-CAAAAAAAAA-CAA
- chr12-8604926-CAAAAAAAAA-CAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAAAAAAA
- chr12-8604926-CAAAAAAAAA-CAAAAAAAAAAAAAA
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_020661.4(AICDA):c.428-13_428-5delTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,249,680 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000056 ( 0 hom. )
Consequence
AICDA
NM_020661.4 splice_region, intron
NM_020661.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.61
Publications
0 publications found
Genes affected
AICDA (HGNC:13203): (activation induced cytidine deaminase) This gene encodes a RNA-editing deaminase that is a member of the cytidine deaminase family. AICDA is specifically expressed and active in germinal center-like B cells. In the germinal center, AICDA is involved in somatic hypermutation, gene conversion, and class-switch recombination of immunoglobulin genes. An epigenetic role in neoplastic transformation and lymphoma progression has been experimentally ascribed to AICDA using mouse models. Defects in this gene are the cause of autosomal recessive hyper-IgM immunodeficiency syndrome type 2 (HIGM2). [provided by RefSeq, Jul 2020]
AICDA Gene-Disease associations (from GenCC):
- hyper-IgM syndrome type 2Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 12-8604926-CAAAAAAAAA-C is Benign according to our data. Variant chr12-8604926-CAAAAAAAAA-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3778339.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020661.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| AICDA | MANE Select | c.428-13_428-5delTTTTTTTTT | splice_region intron | N/A | NP_065712.1 | Q9GZX7-1 | |||
| AICDA | c.428-43_428-35delTTTTTTTTT | intron | N/A | NP_001317272.1 | Q9GZX7-2 | ||||
| AICDA | c.427+280_427+288delTTTTTTTTT | intron | N/A | NP_001397899.1 | Q6QJ80 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AICDA | TSL:1 MANE Select | c.428-13_428-5delTTTTTTTTT | splice_region intron | N/A | ENSP00000229335.6 | Q9GZX7-1 | |||
| AICDA | TSL:1 | c.427+280_427+288delTTTTTTTTT | intron | N/A | ENSP00000439103.2 | Q6QJ80 | |||
| AICDA | TSL:1 | c.157-598_157-590delTTTTTTTTT | intron | N/A | ENSP00000439538.2 | Q6QLN7 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
0
GnomAD4 exome AF: 0.00000560 AC: 7AN: 1249680Hom.: 0 AF XY: 0.00000803 AC XY: 5AN XY: 622912 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1249680
Hom.:
AF XY:
AC XY:
5
AN XY:
622912
show subpopulations
African (AFR)
AF:
AC:
0
AN:
29126
American (AMR)
AF:
AC:
0
AN:
33050
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22258
East Asian (EAS)
AF:
AC:
0
AN:
33854
South Asian (SAS)
AF:
AC:
0
AN:
73714
European-Finnish (FIN)
AF:
AC:
0
AN:
43108
Middle Eastern (MID)
AF:
AC:
0
AN:
3618
European-Non Finnish (NFE)
AF:
AC:
7
AN:
959110
Other (OTH)
AF:
AC:
0
AN:
51842
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.568
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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4
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8
10
<30
30-35
35-40
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
0
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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