16-56961322-C-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.00000302 in 330,668 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000030 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.620
Publications
0 publications found
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
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 |
|---|
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000302 AC: 1AN: 330668Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 188740 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
330668
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
188740
show subpopulations
African (AFR)
AF:
AC:
0
AN:
9770
American (AMR)
AF:
AC:
0
AN:
31412
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11176
East Asian (EAS)
AF:
AC:
0
AN:
11880
South Asian (SAS)
AF:
AC:
0
AN:
61672
European-Finnish (FIN)
AF:
AC:
0
AN:
14782
Middle Eastern (MID)
AF:
AC:
0
AN:
2790
European-Non Finnish (NFE)
AF:
AC:
1
AN:
171930
Other (OTH)
AF:
AC:
0
AN:
15256
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
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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