chr12-88905969-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The variant allele was found at a frequency of 0.364 in 151,972 control chromosomes in the GnomAD database, including 15,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Affects (no stars).
Frequency
Genomes: 𝑓 0.36 ( 15471 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.13
Publications
18 publications found
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ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.
Variant Effect in Transcripts
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Frequencies
GnomAD3 genomes 0.363 AC: 55169AN: 151852Hom.: 15417 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
55169
AN:
151852
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 0.364 AC: 55276AN: 151972Hom.: 15471 Cov.: 32 AF XY: 0.360 AC XY: 26759AN XY: 74282 show subpopulations
GnomAD4 genome
AF:
AC:
55276
AN:
151972
Hom.:
Cov.:
32
AF XY:
AC XY:
26759
AN XY:
74282
show subpopulations
African (AFR)
AF:
AC:
32840
AN:
41432
American (AMR)
AF:
AC:
4277
AN:
15238
Ashkenazi Jewish (ASJ)
AF:
AC:
703
AN:
3468
East Asian (EAS)
AF:
AC:
1077
AN:
5178
South Asian (SAS)
AF:
AC:
854
AN:
4812
European-Finnish (FIN)
AF:
AC:
2663
AN:
10568
Middle Eastern (MID)
AF:
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11949
AN:
67966
Other (OTH)
AF:
AC:
641
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1248
2495
3743
4990
6238
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
440
880
1320
1760
2200
<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:
940
AN:
3478
ClinVar
Significance: Affects
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SKIN/HAIR/EYE PIGMENTATION 7, DARK/LIGHT SKIN Other:1
Dec 14, 2007
OMIM
Significance:Affects
Review Status:no assertion criteria provided
Collection Method:literature only
Computational 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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