rs1015151

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 0.53 in 151,974 control chromosomes in the GnomAD database, including 21,846 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 0.53 ( 21846 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.137

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=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes
AF:
0.529
AC:
80383
AN:
151856
Hom.:
21815
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.621
Gnomad AMI
AF:
0.609
Gnomad AMR
AF:
0.588
Gnomad ASJ
AF:
0.449
Gnomad EAS
AF:
0.697
Gnomad SAS
AF:
0.572
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.525
Gnomad NFE
AF:
0.461
Gnomad OTH
AF:
0.525
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.530
AC:
80475
AN:
151974
Hom.:
21846
Cov.:
32
AF XY:
0.534
AC XY:
39641
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.621
AC:
25733
AN:
41432
American (AMR)
AF:
0.588
AC:
8973
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.449
AC:
1557
AN:
3470
East Asian (EAS)
AF:
0.697
AC:
3604
AN:
5172
South Asian (SAS)
AF:
0.572
AC:
2760
AN:
4822
European-Finnish (FIN)
AF:
0.448
AC:
4718
AN:
10536
Middle Eastern (MID)
AF:
0.527
AC:
154
AN:
292
European-Non Finnish (NFE)
AF:
0.461
AC:
31313
AN:
67960
Other (OTH)
AF:
0.525
AC:
1109
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1918
3836
5754
7672
9590
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
700
1400
2100
2800
3500
<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:
0.504
Hom.:
2399
Bravo
AF:
0.543
Asia WGS
AF:
0.645
AC:
2245
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
9.7
DANN
Benign
0.59
PhyloP100
0.14

Splicing

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

Publications

Other links and lift over

dbSNP: rs1015151; hg19: chr20-6690502; API