GeneBe

rs6038115

Variant names:

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 0.513 in 514,212 control chromosomes in the GnomAD database, including 68,922 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 0.52 ( 20476 hom., cov: 32)
Exomes 𝑓: 0.51 ( 48446 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198

Publications

9 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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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:
0.519
AC:
78768
AN:
151792
Hom.:
20457
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.550
Gnomad AMI
AF:
0.445
Gnomad AMR
AF:
0.474
Gnomad ASJ
AF:
0.509
Gnomad EAS
AF:
0.671
Gnomad SAS
AF:
0.569
Gnomad FIN
AF:
0.520
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.496
Gnomad OTH
AF:
0.511
GnomAD2 exomes
AF:
0.516
AC:
116955
AN:
226788
AF XY:
0.520
show subpopulations
Gnomad AFR exome
AF:
0.546
Gnomad AMR exome
AF:
0.449
Gnomad ASJ exome
AF:
0.502
Gnomad EAS exome
AF:
0.675
Gnomad FIN exome
AF:
0.526
Gnomad NFE exome
AF:
0.492
Gnomad OTH exome
AF:
0.497
GnomAD4 exome
AF:
0.510
AC:
184860
AN:
362302
Hom.:
48446
Cov.:
0
AF XY:
0.516
AC XY:
107235
AN XY:
207826
show subpopulations
African (AFR)
AF:
0.547
AC:
5716
AN:
10442
American (AMR)
AF:
0.448
AC:
16155
AN:
36074
Ashkenazi Jewish (ASJ)
AF:
0.499
AC:
5695
AN:
11412
East Asian (EAS)
AF:
0.665
AC:
8744
AN:
13146
South Asian (SAS)
AF:
0.568
AC:
37416
AN:
65906
European-Finnish (FIN)
AF:
0.512
AC:
8494
AN:
16592
Middle Eastern (MID)
AF:
0.526
AC:
1491
AN:
2836
European-Non Finnish (NFE)
AF:
0.489
AC:
92734
AN:
189484
Other (OTH)
AF:
0.513
AC:
8415
AN:
16410
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.421
Heterozygous variant carriers
0
4524
9048
13571
18095
22619
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
806
1612
2418
3224
4030
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.519
AC:
78834
AN:
151910
Hom.:
20476
Cov.:
32
AF XY:
0.522
AC XY:
38725
AN XY:
74228
show subpopulations
African (AFR)
AF:
0.550
AC:
22777
AN:
41384
American (AMR)
AF:
0.474
AC:
7241
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.509
AC:
1765
AN:
3470
East Asian (EAS)
AF:
0.671
AC:
3477
AN:
5184
South Asian (SAS)
AF:
0.567
AC:
2729
AN:
4814
European-Finnish (FIN)
AF:
0.520
AC:
5480
AN:
10530
Middle Eastern (MID)
AF:
0.514
AC:
151
AN:
294
European-Non Finnish (NFE)
AF:
0.496
AC:
33721
AN:
67932
Other (OTH)
AF:
0.515
AC:
1087
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1959
3918
5876
7835
9794
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
708
1416
2124
2832
3540
<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:
0.507
Hom.:
4473
Bravo
AF:
0.514
Asia WGS
AF:
0.601
AC:
2087
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.4
DANN
Benign
0.39
PhyloP100
-0.20

Splicing

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

Publications

Other links and lift over

dbSNP: rs6038115; hg19: chr20-5261132; API