GeneBe

chr21-33401191-T-TG

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 0.246 in 152,032 control chromosomes in the GnomAD database, including 6,386 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 6386 hom., cov: 25)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.249

Publications

3 publications found
Variant links:

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ACMG classification

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

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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:
0.246
AC:
37363
AN:
151914
Hom.:
6370
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.465
Gnomad AMI
AF:
0.106
Gnomad AMR
AF:
0.178
Gnomad ASJ
AF:
0.129
Gnomad EAS
AF:
0.422
Gnomad SAS
AF:
0.289
Gnomad FIN
AF:
0.190
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.130
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.246
AC:
37416
AN:
152032
Hom.:
6386
Cov.:
25
AF XY:
0.247
AC XY:
18335
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.466
AC:
19300
AN:
41432
American (AMR)
AF:
0.177
AC:
2708
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.129
AC:
448
AN:
3472
East Asian (EAS)
AF:
0.422
AC:
2176
AN:
5156
South Asian (SAS)
AF:
0.287
AC:
1385
AN:
4826
European-Finnish (FIN)
AF:
0.190
AC:
2006
AN:
10582
Middle Eastern (MID)
AF:
0.119
AC:
35
AN:
294
European-Non Finnish (NFE)
AF:
0.130
AC:
8841
AN:
67980
Other (OTH)
AF:
0.198
AC:
420
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1243
2486
3728
4971
6214
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
370
740
1110
1480
1850
<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:
0.194
Hom.:
527
Bravo
AF:
0.257
Asia WGS
AF:
0.389
AC:
1348
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.25

Splicing

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

Publications

Other links and lift over

dbSNP: rs17880053; hg19: chr21-34773497; API