GeneBe

22-22180754-A-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 0.349 in 151,816 control chromosomes in the GnomAD database, including 9,614 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 0.35 ( 9614 hom., cov: 33)

Consequence

IGL
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378

Publications

1 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGL n.22180754A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.349
AC:
52930
AN:
151704
Hom.:
9597
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.318
Gnomad AMI
AF:
0.327
Gnomad AMR
AF:
0.437
Gnomad ASJ
AF:
0.279
Gnomad EAS
AF:
0.659
Gnomad SAS
AF:
0.488
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.318
Gnomad OTH
AF:
0.340
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.349
AC:
52994
AN:
151816
Hom.:
9614
Cov.:
33
AF XY:
0.357
AC XY:
26520
AN XY:
74204
show subpopulations
African (AFR)
AF:
0.319
AC:
13217
AN:
41406
American (AMR)
AF:
0.437
AC:
6663
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.279
AC:
964
AN:
3460
East Asian (EAS)
AF:
0.658
AC:
3374
AN:
5128
South Asian (SAS)
AF:
0.488
AC:
2348
AN:
4808
European-Finnish (FIN)
AF:
0.356
AC:
3748
AN:
10534
Middle Eastern (MID)
AF:
0.291
AC:
85
AN:
292
European-Non Finnish (NFE)
AF:
0.318
AC:
21572
AN:
67920
Other (OTH)
AF:
0.344
AC:
725
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1775
3550
5326
7101
8876
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
518
1036
1554
2072
2590
<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:
0.351
Hom.:
3392
Bravo
AF:
0.356
Asia WGS
AF:
0.564
AC:
1958
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.8
DANN
Benign
0.66
PhyloP100
0.38

Splicing

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

Publications

Other links and lift over

dbSNP: rs713624; hg19: chr22-22535144; API