19-54288907-C-G
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 0.76 in 151,540 control chromosomes in the GnomAD database, including 44,793 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 0.76 ( 44780 hom., cov: 31)
Exomes 𝑓: 0.80 ( 13 hom. )
Consequence
Unknown
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.22
Publications
82 publications found
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (Cadd=0.033).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.
Variant Effect in Transcripts
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Frequencies
GnomAD3 genomes 0.761 AC: 115131AN: 151382Hom.: 44749 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
115131
AN:
151382
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 0.800 AC: 32AN: 40Hom.: 13 Cov.: 0 AF XY: 0.800 AC XY: 24AN XY: 30 show subpopulations
GnomAD4 exome
AF:
AC:
32
AN:
40
Hom.:
Cov.:
0
AF XY:
AC XY:
24
AN XY:
30
show subpopulations
African (AFR)
AF:
AC:
2
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
2
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
7
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
20
AN:
26
Other (OTH)
AF:
AC:
1
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.760 AC: 115213AN: 151500Hom.: 44780 Cov.: 31 AF XY: 0.752 AC XY: 55673AN XY: 74022 show subpopulations
GnomAD4 genome
AF:
AC:
115213
AN:
151500
Hom.:
Cov.:
31
AF XY:
AC XY:
55673
AN XY:
74022
show subpopulations
African (AFR)
AF:
AC:
33626
AN:
41230
American (AMR)
AF:
AC:
9438
AN:
15234
Ashkenazi Jewish (ASJ)
AF:
AC:
3147
AN:
3456
East Asian (EAS)
AF:
AC:
1687
AN:
5148
South Asian (SAS)
AF:
AC:
3942
AN:
4814
European-Finnish (FIN)
AF:
AC:
7100
AN:
10468
Middle Eastern (MID)
AF:
AC:
261
AN:
294
European-Non Finnish (NFE)
AF:
AC:
53541
AN:
67836
Other (OTH)
AF:
AC:
1662
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1365
2731
4096
5462
6827
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
844
1688
2532
3376
4220
<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:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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