11-105047405-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000525374.1(CARD16):n.25-2747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,080 control chromosomes in the GnomAD database, including 959 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 0.092 ( 959 hom., cov: 32)
Consequence
CARD16
ENST00000525374.1 intron
ENST00000525374.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.129
Publications
3 publications found
Genes affected
CARD16 (HGNC:33701): (caspase recruitment domain family member 16) Enables several functions, including CARD domain binding activity; cysteine-type endopeptidase inhibitor activity; and enzyme binding activity. Involved in several processes, including negative regulation of cysteine-type endopeptidase activity; regulation of gene expression; and regulation of signal transduction. Part of protease inhibitor complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0918 AC: 13948AN: 151962Hom.: 958 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
13948
AN:
151962
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: 0.0917 AC: 13949AN: 152080Hom.: 959 Cov.: 32 AF XY: 0.0964 AC XY: 7167AN XY: 74324 show subpopulations
GnomAD4 genome
AF:
AC:
13949
AN:
152080
Hom.:
Cov.:
32
AF XY:
AC XY:
7167
AN XY:
74324
show subpopulations
African (AFR)
AF:
AC:
857
AN:
41514
American (AMR)
AF:
AC:
3252
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
369
AN:
3470
East Asian (EAS)
AF:
AC:
25
AN:
5172
South Asian (SAS)
AF:
AC:
483
AN:
4804
European-Finnish (FIN)
AF:
AC:
1500
AN:
10570
Middle Eastern (MID)
AF:
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7069
AN:
67972
Other (OTH)
AF:
AC:
235
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
606
1212
1817
2423
3029
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
160
320
480
640
800
<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:
208
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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