chr1-74988307-G-A
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 0.144 in 152,232 control chromosomes in the GnomAD database, including 1,924 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 0.14 ( 1924 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.123
Publications
0 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=-0.97).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 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: 0.144 AC: 21849AN: 152114Hom.: 1922 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21849
AN:
152114
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: 0.144 AC: 21855AN: 152232Hom.: 1924 Cov.: 32 AF XY: 0.147 AC XY: 10924AN XY: 74428 show subpopulations
GnomAD4 genome
AF:
AC:
21855
AN:
152232
Hom.:
Cov.:
32
AF XY:
AC XY:
10924
AN XY:
74428
show subpopulations
African (AFR)
AF:
AC:
2097
AN:
41566
American (AMR)
AF:
AC:
3439
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
443
AN:
3468
East Asian (EAS)
AF:
AC:
706
AN:
5170
South Asian (SAS)
AF:
AC:
1528
AN:
4832
European-Finnish (FIN)
AF:
AC:
1618
AN:
10598
Middle Eastern (MID)
AF:
AC:
35
AN:
292
European-Non Finnish (NFE)
AF:
AC:
11571
AN:
68006
Other (OTH)
AF:
AC:
299
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
927
1854
2782
3709
4636
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
258
516
774
1032
1290
<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:
760
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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