GeneBe

chr20-45173959-GT-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.154 in 149,250 control chromosomes in the GnomAD database, including 1,876 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1876 hom., cov: 28)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.750

Publications

1 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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:
0.154
AC:
22983
AN:
149118
Hom.:
1871
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.209
Gnomad EAS
AF:
0.0377
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.229
Gnomad NFE
AF:
0.175
Gnomad OTH
AF:
0.165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.154
AC:
23022
AN:
149250
Hom.:
1876
Cov.:
28
AF XY:
0.155
AC XY:
11298
AN XY:
72880
show subpopulations
African (AFR)
AF:
0.123
AC:
5014
AN:
40886
American (AMR)
AF:
0.132
AC:
1963
AN:
14892
Ashkenazi Jewish (ASJ)
AF:
0.209
AC:
723
AN:
3454
East Asian (EAS)
AF:
0.0378
AC:
180
AN:
4768
South Asian (SAS)
AF:
0.154
AC:
681
AN:
4422
European-Finnish (FIN)
AF:
0.194
AC:
1966
AN:
10152
Middle Eastern (MID)
AF:
0.240
AC:
70
AN:
292
European-Non Finnish (NFE)
AF:
0.175
AC:
11789
AN:
67382
Other (OTH)
AF:
0.168
AC:
352
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.480
Heterozygous variant carriers
0
864
1727
2591
3454
4318
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
252
504
756
1008
1260
<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:
0.165
Hom.:
249
Bravo
AF:
0.146
Asia WGS
AF:
0.0930
AC:
322
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56387543; hg19: chr20-43802600; API