GeneBe

rs5756208

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 0.76 in 151,922 control chromosomes in the GnomAD database, including 44,786 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 0.76 ( 44760 hom., cov: 30)
Exomes 𝑓: 0.74 ( 26 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60

Publications

3 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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 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:
0.760
AC:
115256
AN:
151712
Hom.:
44735
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
0.868
Gnomad AMR
AF:
0.793
Gnomad ASJ
AF:
0.799
Gnomad EAS
AF:
0.260
Gnomad SAS
AF:
0.522
Gnomad FIN
AF:
0.723
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.813
Gnomad OTH
AF:
0.765
GnomAD4 exome
AF:
0.739
AC:
68
AN:
92
Hom.:
26
Cov.:
0
AF XY:
0.697
AC XY:
46
AN XY:
66
show subpopulations
African (AFR)
AF:
1.00
AC:
2
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.553
AC:
21
AN:
38
European-Finnish (FIN)
AF:
0.500
AC:
1
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.913
AC:
42
AN:
46
Other (OTH)
AF:
0.500
AC:
2
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.760
AC:
115335
AN:
151830
Hom.:
44760
Cov.:
30
AF XY:
0.751
AC XY:
55677
AN XY:
74186
show subpopulations
African (AFR)
AF:
0.753
AC:
31167
AN:
41388
American (AMR)
AF:
0.793
AC:
12102
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.799
AC:
2771
AN:
3468
East Asian (EAS)
AF:
0.260
AC:
1335
AN:
5132
South Asian (SAS)
AF:
0.522
AC:
2508
AN:
4808
European-Finnish (FIN)
AF:
0.723
AC:
7614
AN:
10526
Middle Eastern (MID)
AF:
0.793
AC:
233
AN:
294
European-Non Finnish (NFE)
AF:
0.813
AC:
55220
AN:
67934
Other (OTH)
AF:
0.760
AC:
1597
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1302
2603
3905
5206
6508
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
846
1692
2538
3384
4230
<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:
0.729
Hom.:
1690
Bravo
AF:
0.765
Asia WGS
AF:
0.420
AC:
1463
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.3
DANN
Benign
0.39
PhyloP100
-1.6
PromoterAI
-0.051
Neutral
Mutation Taster
=300/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs5756208; hg19: chr22-36878042; API