rs16944
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.573 in 152,000 control chromosomes in the GnomAD database, including 25,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.57 ( 25795 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.560
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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 |
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Frequencies
GnomAD3 genomes AF: 0.574 AC: 87133AN: 151882Hom.: 25788 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
87133
AN:
151882
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: 0.573 AC: 87156AN: 152000Hom.: 25795 Cov.: 32 AF XY: 0.566 AC XY: 42063AN XY: 74286 show subpopulations
GnomAD4 genome
AF:
AC:
87156
AN:
152000
Hom.:
Cov.:
32
AF XY:
AC XY:
42063
AN XY:
74286
Gnomad4 AFR
AF:
AC:
0.455748
AN:
0.455748
Gnomad4 AMR
AF:
AC:
0.498559
AN:
0.498559
Gnomad4 ASJ
AF:
AC:
0.651498
AN:
0.651498
Gnomad4 EAS
AF:
AC:
0.537427
AN:
0.537427
Gnomad4 SAS
AF:
AC:
0.405019
AN:
0.405019
Gnomad4 FIN
AF:
AC:
0.596957
AN:
0.596957
Gnomad4 NFE
AF:
AC:
0.666039
AN:
0.666039
Gnomad4 OTH
AF:
AC:
0.581835
AN:
0.581835
Heterozygous variant carriers
0
1867
3734
5601
7468
9335
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
730
1460
2190
2920
3650
<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:
1587
AN:
3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Antisynthetase syndrome Other:1
Feb 11, 2020
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas
Significance:association
Review Status:no assertion criteria provided
Collection Method:case-control
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at