chr20-3677564-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025220.5(ADAM33):c.178-421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,104 control chromosomes in the GnomAD database, including 41,242 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 0.74 ( 41242 hom., cov: 32)
Consequence
ADAM33
NM_025220.5 intron
NM_025220.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.823
Publications
9 publications found
Genes affected
ADAM33 (HGNC:15478): (ADAM metallopeptidase domain 33) This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. This protein is a type I transmembrane protein implicated in asthma and bronchial hyperresponsiveness. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
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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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAM33 | ENST00000356518.7 | c.178-421A>G | intron_variant | Intron 2 of 21 | 1 | NM_025220.5 | ENSP00000348912.3 | |||
ADAM33 | ENST00000379861.8 | c.178-421A>G | intron_variant | Intron 2 of 21 | 1 | ENSP00000369190.4 | ||||
ADAM33 | ENST00000350009.6 | c.178-421A>G | intron_variant | Intron 2 of 20 | 5 | ENSP00000322550.5 |
Frequencies
GnomAD3 genomes AF: 0.736 AC: 111858AN: 151986Hom.: 41228 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
111858
AN:
151986
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: 0.736 AC: 111911AN: 152104Hom.: 41242 Cov.: 32 AF XY: 0.733 AC XY: 54535AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
111911
AN:
152104
Hom.:
Cov.:
32
AF XY:
AC XY:
54535
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
28913
AN:
41492
American (AMR)
AF:
AC:
11510
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
2492
AN:
3472
East Asian (EAS)
AF:
AC:
4027
AN:
5158
South Asian (SAS)
AF:
AC:
3454
AN:
4820
European-Finnish (FIN)
AF:
AC:
7434
AN:
10592
Middle Eastern (MID)
AF:
AC:
197
AN:
294
European-Non Finnish (NFE)
AF:
AC:
51624
AN:
67974
Other (OTH)
AF:
AC:
1545
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1523
3046
4569
6092
7615
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
846
1692
2538
3384
4230
<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:
2714
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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