GeneBe

rs955396

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 0.0731 in 290,254 control chromosomes in the GnomAD database, including 927 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 0.079 ( 513 hom., cov: 33)
Exomes 𝑓: 0.067 ( 414 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702

Publications

1 publications found
Variant links:

Genome browser will be placed here

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 (AMR) allele frequency at 95% confidence interval = 0.116 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:
0.0788
AC:
11991
AN:
152088
Hom.:
513
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0853
Gnomad AMI
AF:
0.0932
Gnomad AMR
AF:
0.120
Gnomad ASJ
AF:
0.0455
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.0575
Gnomad FIN
AF:
0.103
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0713
Gnomad OTH
AF:
0.0693
GnomAD4 exome
AF:
0.0668
AC:
9220
AN:
138048
Hom.:
414
AF XY:
0.0655
AC XY:
5001
AN XY:
76340
show subpopulations
African (AFR)
AF:
0.0828
AC:
227
AN:
2742
American (AMR)
AF:
0.133
AC:
584
AN:
4376
Ashkenazi Jewish (ASJ)
AF:
0.0360
AC:
115
AN:
3194
East Asian (EAS)
AF:
0.00127
AC:
5
AN:
3936
South Asian (SAS)
AF:
0.0595
AC:
1632
AN:
27438
European-Finnish (FIN)
AF:
0.0801
AC:
852
AN:
10636
Middle Eastern (MID)
AF:
0.0370
AC:
31
AN:
838
European-Non Finnish (NFE)
AF:
0.0683
AC:
5339
AN:
78206
Other (OTH)
AF:
0.0651
AC:
435
AN:
6682
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
409
818
1227
1636
2045
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
34
68
102
136
170
<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:
0.0788
AC:
11997
AN:
152206
Hom.:
513
Cov.:
33
AF XY:
0.0812
AC XY:
6047
AN XY:
74436
show subpopulations
African (AFR)
AF:
0.0852
AC:
3535
AN:
41514
American (AMR)
AF:
0.120
AC:
1841
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.0455
AC:
158
AN:
3470
East Asian (EAS)
AF:
0.00173
AC:
9
AN:
5188
South Asian (SAS)
AF:
0.0573
AC:
276
AN:
4814
European-Finnish (FIN)
AF:
0.103
AC:
1092
AN:
10604
Middle Eastern (MID)
AF:
0.0238
AC:
7
AN:
294
European-Non Finnish (NFE)
AF:
0.0713
AC:
4849
AN:
68008
Other (OTH)
AF:
0.0686
AC:
145
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
569
1138
1706
2275
2844
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
134
268
402
536
670
<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:
0.0778
Hom.:
77
Bravo
AF:
0.0814
Asia WGS
AF:
0.0310
AC:
109
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
6.7
DANN
Benign
0.23
PhyloP100
0.70

Splicing

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

Publications

Other links and lift over

dbSNP: rs955396; hg19: chr11-1288876; API