11-105047405-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.129

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CARD16ENST00000525374.1 linkn.25-2747A>G intron_variant Intron 1 of 3 3
ENSG00000303891ENST00000797905.1 linkn.746-10955T>C intron_variant Intron 6 of 8

Frequencies

GnomAD3 genomes
AF:
0.0918
AC:
13948
AN:
151962
Hom.:
958
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0207
Gnomad AMI
AF:
0.135
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.106
Gnomad EAS
AF:
0.00463
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.104
Gnomad OTH
AF:
0.113
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0917
AC:
13949
AN:
152080
Hom.:
959
Cov.:
32
AF XY:
0.0964
AC XY:
7167
AN XY:
74324
show subpopulations
African (AFR)
AF:
0.0206
AC:
857
AN:
41514
American (AMR)
AF:
0.213
AC:
3252
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.106
AC:
369
AN:
3470
East Asian (EAS)
AF:
0.00483
AC:
25
AN:
5172
South Asian (SAS)
AF:
0.101
AC:
483
AN:
4804
European-Finnish (FIN)
AF:
0.142
AC:
1500
AN:
10570
Middle Eastern (MID)
AF:
0.122
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
0.104
AC:
7069
AN:
67972
Other (OTH)
AF:
0.111
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:
0.0991
Hom.:
301
Bravo
AF:
0.0948
Asia WGS
AF:
0.0600
AC:
208
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.8
DANN
Benign
0.35
PhyloP100
-0.13
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs501626; hg19: chr11-104918132; API