Genetic Variant AICDA:c.428-11_428-5delTTTTTTT (chr12-8604926-CAAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_020661.4(AICDA):c.428-11_428-5delTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000865 in 1,386,516 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000073 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000088 ( 0 hom. )

Consequence

AICDA
NM_020661.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.61

Publications

3 publications found

Variant links:

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 2
Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics

AICDA links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AICDA	NM_020661.4	MANE Select	c.428-11_428-5delTTTTTTT	splice_region intron	N/A	NP_065712.1	Q9GZX7-1
AICDA	NM_001330343.2		c.428-41_428-35delTTTTTTT	intron	N/A	NP_001317272.1	Q9GZX7-2
AICDA	NM_001410970.1		c.427+282_427+288delTTTTTTT	intron	N/A	NP_001397899.1	Q6QJ80

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AICDA	ENST00000229335.11	TSL:1 MANE Select	c.428-11_428-5delTTTTTTT	splice_region intron	N/A	ENSP00000229335.6	Q9GZX7-1
AICDA	ENST00000543081.6	TSL:1	c.427+282_427+288delTTTTTTT	intron	N/A	ENSP00000439103.2	Q6QJ80
AICDA	ENST00000544516.6	TSL:1	c.157-596_157-590delTTTTTTT	intron	N/A	ENSP00000439538.2	Q6QLN7

Frequencies

GnomAD3 genomes

AF:

0.00000731

AC:

AN:

136836

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000207

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000880

AC:

AN:

1249680

Hom.:

AF XY:

0.00000642

AC XY:

AN XY:

622912

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29126

American (AMR)

AF:

0.00

AC:

AN:

33050

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22258

East Asian (EAS)

AF:

0.000295

AC:

AN:

33854

South Asian (SAS)

AF:

0.00

AC:

AN:

73714

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43108

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3618

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

959110

Other (OTH)

AF:

0.0000193

AC:

AN:

51842

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.570

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

AF:

0.00000731

AC:

AN:

136836

Hom.:

Cov.:

AF XY:

0.0000153

AC XY:

AN XY:

65504

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

36512

American (AMR)

AF:

0.00

AC:

AN:

13632

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3350

East Asian (EAS)

AF:

0.000207

AC:

AN:

4828

South Asian (SAS)

AF:

0.00

AC:

AN:

4324

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6584

Middle Eastern (MID)

AF:

0.00

AC:

AN:

296

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64562

Other (OTH)

AF:

0.00

AC:

AN:

1856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over