rs892188

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 0.312 in 151,966 control chromosomes in the GnomAD database, including 8,981 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 0.31 ( 8981 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.684

Publications

18 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=-1.04).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 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:
0.312
AC:
47435
AN:
151848
Hom.:
8983
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0947
Gnomad AMI
AF:
0.562
Gnomad AMR
AF:
0.462
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.403
Gnomad FIN
AF:
0.361
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.395
Gnomad OTH
AF:
0.357
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.312
AC:
47429
AN:
151966
Hom.:
8981
Cov.:
31
AF XY:
0.314
AC XY:
23294
AN XY:
74268
show subpopulations
African (AFR)
AF:
0.0943
AC:
3915
AN:
41496
American (AMR)
AF:
0.462
AC:
7045
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.377
AC:
1306
AN:
3468
East Asian (EAS)
AF:
0.242
AC:
1246
AN:
5154
South Asian (SAS)
AF:
0.404
AC:
1944
AN:
4812
European-Finnish (FIN)
AF:
0.361
AC:
3800
AN:
10532
Middle Eastern (MID)
AF:
0.361
AC:
106
AN:
294
European-Non Finnish (NFE)
AF:
0.395
AC:
26804
AN:
67928
Other (OTH)
AF:
0.357
AC:
753
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
1512
3025
4537
6050
7562
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
472
944
1416
1888
2360
<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:
0.338
Hom.:
2240
Bravo
AF:
0.312
Asia WGS
AF:
0.333
AC:
1162
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.44
PhyloP100
-0.68

Splicing

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

Publications

Other links and lift over

dbSNP: rs892188; hg19: chr19-10409793; API