3-186831295-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 0.362 in 151,800 control chromosomes in the GnomAD database, including 10,481 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 0.36 ( 10481 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

1 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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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:
0.362
AC:
54877
AN:
151682
Hom.:
10474
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.303
Gnomad AMI
AF:
0.515
Gnomad AMR
AF:
0.419
Gnomad ASJ
AF:
0.362
Gnomad EAS
AF:
0.442
Gnomad SAS
AF:
0.362
Gnomad FIN
AF:
0.555
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.345
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.362
AC:
54918
AN:
151800
Hom.:
10481
Cov.:
31
AF XY:
0.372
AC XY:
27551
AN XY:
74140
show subpopulations
African (AFR)
AF:
0.303
AC:
12506
AN:
41338
American (AMR)
AF:
0.419
AC:
6400
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.362
AC:
1256
AN:
3470
East Asian (EAS)
AF:
0.442
AC:
2269
AN:
5130
South Asian (SAS)
AF:
0.361
AC:
1737
AN:
4806
European-Finnish (FIN)
AF:
0.555
AC:
5841
AN:
10518
Middle Eastern (MID)
AF:
0.298
AC:
87
AN:
292
European-Non Finnish (NFE)
AF:
0.348
AC:
23623
AN:
67962
Other (OTH)
AF:
0.346
AC:
730
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1746
3492
5237
6983
8729
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
534
1068
1602
2136
2670
<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:
0.230
Hom.:
560
Bravo
AF:
0.350
Asia WGS
AF:
0.423
AC:
1474
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
0.49
DANN
Benign
0.34
PhyloP100
-1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs12631446; hg19: chr3-186549084; API