GeneBe

rs798887

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 149,610 control chromosomes in the GnomAD database, including 44,296 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 ( 44296 hom., cov: 25)
Exomes 𝑓: 0.25 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

Unknown

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

17 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=-1.09).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 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:
113690
AN:
149498
Hom.:
44266
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.815
Gnomad AMI
AF:
0.889
Gnomad AMR
AF:
0.619
Gnomad ASJ
AF:
0.910
Gnomad EAS
AF:
0.329
Gnomad SAS
AF:
0.817
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.895
Gnomad NFE
AF:
0.790
Gnomad OTH
AF:
0.788
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.250
AC:
2
AN:
8
Hom.:
0
Cov.:
0
AF XY:
0.250
AC XY:
1
AN XY:
4
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.500
AC:
2
AN:
4
Other (OTH)
AC:
0
AN:
0
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.350
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.760
AC:
113768
AN:
149610
Hom.:
44296
Cov.:
25
AF XY:
0.752
AC XY:
54858
AN XY:
72940
show subpopulations
African (AFR)
AF:
0.815
AC:
33163
AN:
40684
American (AMR)
AF:
0.618
AC:
9241
AN:
14954
Ashkenazi Jewish (ASJ)
AF:
0.910
AC:
3119
AN:
3428
East Asian (EAS)
AF:
0.328
AC:
1686
AN:
5136
South Asian (SAS)
AF:
0.817
AC:
3829
AN:
4684
European-Finnish (FIN)
AF:
0.677
AC:
6936
AN:
10246
Middle Eastern (MID)
AF:
0.894
AC:
261
AN:
292
European-Non Finnish (NFE)
AF:
0.790
AC:
53103
AN:
67218
Other (OTH)
AF:
0.788
AC:
1623
AN:
2060
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
1143
2286
3430
4573
5716
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
834
1668
2502
3336
4170
<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:
0.798
Hom.:
66427
Bravo
AF:
0.750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.17
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs798887; hg19: chr19-54793188; API