GeneBe

11-113974819-A-G

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 0.892 in 287,354 control chromosomes in the GnomAD database, including 115,756 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 0.86 ( 57429 hom., cov: 29)
Exomes 𝑓: 0.93 ( 58327 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

33 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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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:
0.862
AC:
130861
AN:
151792
Hom.:
57406
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.682
Gnomad AMI
AF:
0.879
Gnomad AMR
AF:
0.913
Gnomad ASJ
AF:
0.969
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.958
Gnomad FIN
AF:
0.967
Gnomad MID
AF:
0.889
Gnomad NFE
AF:
0.920
Gnomad OTH
AF:
0.877
GnomAD4 exome
AF:
0.926
AC:
125441
AN:
135448
Hom.:
58327
AF XY:
0.929
AC XY:
66235
AN XY:
71298
show subpopulations
African (AFR)
AF:
0.663
AC:
3022
AN:
4558
American (AMR)
AF:
0.926
AC:
6442
AN:
6956
Ashkenazi Jewish (ASJ)
AF:
0.972
AC:
3180
AN:
3270
East Asian (EAS)
AF:
1.00
AC:
6830
AN:
6832
South Asian (SAS)
AF:
0.955
AC:
20622
AN:
21584
European-Finnish (FIN)
AF:
0.966
AC:
6353
AN:
6574
Middle Eastern (MID)
AF:
0.937
AC:
459
AN:
490
European-Non Finnish (NFE)
AF:
0.922
AC:
72014
AN:
78128
Other (OTH)
AF:
0.924
AC:
6519
AN:
7056
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
416
833
1249
1666
2082
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
430
860
1290
1720
2150
<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:
0.862
AC:
130935
AN:
151906
Hom.:
57429
Cov.:
29
AF XY:
0.867
AC XY:
64371
AN XY:
74230
show subpopulations
African (AFR)
AF:
0.681
AC:
28158
AN:
41326
American (AMR)
AF:
0.914
AC:
13960
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.969
AC:
3364
AN:
3470
East Asian (EAS)
AF:
0.999
AC:
5139
AN:
5142
South Asian (SAS)
AF:
0.958
AC:
4599
AN:
4800
European-Finnish (FIN)
AF:
0.967
AC:
10236
AN:
10582
Middle Eastern (MID)
AF:
0.901
AC:
263
AN:
292
European-Non Finnish (NFE)
AF:
0.920
AC:
62563
AN:
67996
Other (OTH)
AF:
0.878
AC:
1851
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
807
1614
2422
3229
4036
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
884
1768
2652
3536
4420
<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:
0.897
Hom.:
197225
Bravo
AF:
0.850
Asia WGS
AF:
0.964
AC:
3354
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.48
DANN
Benign
0.72
PhyloP100
-1.5
PromoterAI
0.0030
Neutral
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs1150226; hg19: chr11-113845541; API