chr4-140569265-T-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 0.376 in 152,162 control chromosomes in the GnomAD database, including 12,669 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 0.38 ( 12669 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.68
Publications
13 publications found
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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 |
---|
Frequencies
GnomAD3 genomes AF: 0.375 AC: 57066AN: 152044Hom.: 12645 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
57066
AN:
152044
Hom.:
Cov.:
33
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: 0.376 AC: 57140AN: 152162Hom.: 12669 Cov.: 33 AF XY: 0.378 AC XY: 28132AN XY: 74372 show subpopulations
GnomAD4 genome
AF:
AC:
57140
AN:
152162
Hom.:
Cov.:
33
AF XY:
AC XY:
28132
AN XY:
74372
show subpopulations
African (AFR)
AF:
AC:
25313
AN:
41530
American (AMR)
AF:
AC:
5722
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
AC:
1041
AN:
3468
East Asian (EAS)
AF:
AC:
2605
AN:
5134
South Asian (SAS)
AF:
AC:
1962
AN:
4830
European-Finnish (FIN)
AF:
AC:
2687
AN:
10598
Middle Eastern (MID)
AF:
AC:
87
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16731
AN:
67982
Other (OTH)
AF:
AC:
750
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1691
3382
5072
6763
8454
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
528
1056
1584
2112
2640
<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:
1628
AN:
3478
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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