chr2-52476452-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 0.455 in 151,854 control chromosomes in the GnomAD database, including 16,029 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 0.46 ( 16029 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.543

Publications

6 publications found
Variant links:

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ACMG classification

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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:
0.455
AC:
69082
AN:
151736
Hom.:
16022
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.383
Gnomad AMI
AF:
0.571
Gnomad AMR
AF:
0.378
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.534
Gnomad SAS
AF:
0.474
Gnomad FIN
AF:
0.532
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.500
Gnomad OTH
AF:
0.449
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.455
AC:
69121
AN:
151854
Hom.:
16029
Cov.:
31
AF XY:
0.453
AC XY:
33643
AN XY:
74216
show subpopulations
African (AFR)
AF:
0.383
AC:
15847
AN:
41390
American (AMR)
AF:
0.377
AC:
5754
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
0.393
AC:
1363
AN:
3472
East Asian (EAS)
AF:
0.533
AC:
2742
AN:
5140
South Asian (SAS)
AF:
0.473
AC:
2280
AN:
4816
European-Finnish (FIN)
AF:
0.532
AC:
5601
AN:
10532
Middle Eastern (MID)
AF:
0.378
AC:
111
AN:
294
European-Non Finnish (NFE)
AF:
0.500
AC:
33951
AN:
67940
Other (OTH)
AF:
0.452
AC:
952
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1913
3825
5738
7650
9563
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
642
1284
1926
2568
3210
<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:
0.477
Hom.:
67429
Bravo
AF:
0.437
Asia WGS
AF:
0.487
AC:
1690
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
10
DANN
Benign
0.77
PhyloP100
0.54

Splicing

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

Publications

Other links and lift over

dbSNP: rs12619788; hg19: chr2-52703590; API