3-55447047-G-T

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 0.152 in 152,058 control chromosomes in the GnomAD database, including 2,344 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 0.15 ( 2344 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.65

Publications

8 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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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:
0.153
AC:
23184
AN:
151942
Hom.:
2345
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0515
Gnomad AMI
AF:
0.321
Gnomad AMR
AF:
0.130
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.00309
Gnomad SAS
AF:
0.0731
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.152
AC:
23175
AN:
152058
Hom.:
2344
Cov.:
32
AF XY:
0.147
AC XY:
10901
AN XY:
74308
show subpopulations
African (AFR)
AF:
0.0513
AC:
2128
AN:
41492
American (AMR)
AF:
0.130
AC:
1982
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.151
AC:
523
AN:
3470
East Asian (EAS)
AF:
0.00309
AC:
16
AN:
5172
South Asian (SAS)
AF:
0.0725
AC:
349
AN:
4814
European-Finnish (FIN)
AF:
0.177
AC:
1868
AN:
10556
Middle Eastern (MID)
AF:
0.139
AC:
41
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15618
AN:
67970
Other (OTH)
AF:
0.170
AC:
357
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
981
1961
2942
3922
4903
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
256
512
768
1024
1280
<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:
0.182
Hom.:
1529
Bravo
AF:
0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.0030
DANN
Benign
0.55
PhyloP100
-2.7

Splicing

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

Publications

Other links and lift over

dbSNP: rs3913369; hg19: chr3-55481075; API