21-33091332-G-A

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 0.705 in 152,174 control chromosomes in the GnomAD database, including 37,986 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 0.70 ( 37986 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510

Publications

7 publications found
Variant links:

Genome browser will be placed here

ACMG classification

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 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:
0.705
AC:
107161
AN:
152056
Hom.:
37951
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.759
Gnomad AMI
AF:
0.749
Gnomad AMR
AF:
0.743
Gnomad ASJ
AF:
0.740
Gnomad EAS
AF:
0.648
Gnomad SAS
AF:
0.700
Gnomad FIN
AF:
0.639
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.674
Gnomad OTH
AF:
0.736
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.705
AC:
107255
AN:
152174
Hom.:
37986
Cov.:
33
AF XY:
0.704
AC XY:
52378
AN XY:
74384
show subpopulations
African (AFR)
AF:
0.759
AC:
31517
AN:
41528
American (AMR)
AF:
0.743
AC:
11359
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.740
AC:
2569
AN:
3470
East Asian (EAS)
AF:
0.648
AC:
3355
AN:
5178
South Asian (SAS)
AF:
0.700
AC:
3380
AN:
4826
European-Finnish (FIN)
AF:
0.639
AC:
6746
AN:
10562
Middle Eastern (MID)
AF:
0.840
AC:
247
AN:
294
European-Non Finnish (NFE)
AF:
0.674
AC:
45837
AN:
68002
Other (OTH)
AF:
0.740
AC:
1562
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1704
3408
5111
6815
8519
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
836
1672
2508
3344
4180
<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:
0.688
Hom.:
139055
Bravo
AF:
0.713
Asia WGS
AF:
0.673
AC:
2341
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.5
DANN
Benign
0.23
PhyloP100
0.051

Splicing

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

Publications

Other links and lift over

dbSNP: rs7276171; hg19: chr21-34463638; API