GeneBe

rs9288087

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 0.219 in 152,182 control chromosomes in the GnomAD database, including 4,547 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 0.22 ( 4543 hom., cov: 31)
Exomes 𝑓: 0.21 ( 4 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0650

Publications

5 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=-0.78).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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:
0.219
AC:
33320
AN:
151968
Hom.:
4536
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0776
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.254
Gnomad ASJ
AF:
0.197
Gnomad EAS
AF:
0.446
Gnomad SAS
AF:
0.404
Gnomad FIN
AF:
0.331
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.220
GnomAD4 exome
AF:
0.208
AC:
20
AN:
96
Hom.:
4
AF XY:
0.188
AC XY:
12
AN XY:
64
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.238
AC:
20
AN:
84
Other (OTH)
AF:
0.00
AC:
0
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.471
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.219
AC:
33340
AN:
152086
Hom.:
4543
Cov.:
31
AF XY:
0.228
AC XY:
16930
AN XY:
74318
show subpopulations
African (AFR)
AF:
0.0775
AC:
3221
AN:
41540
American (AMR)
AF:
0.254
AC:
3890
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.197
AC:
683
AN:
3470
East Asian (EAS)
AF:
0.447
AC:
2293
AN:
5128
South Asian (SAS)
AF:
0.405
AC:
1950
AN:
4810
European-Finnish (FIN)
AF:
0.331
AC:
3504
AN:
10572
Middle Eastern (MID)
AF:
0.194
AC:
57
AN:
294
European-Non Finnish (NFE)
AF:
0.251
AC:
17028
AN:
67948
Other (OTH)
AF:
0.222
AC:
469
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1251
2502
3753
5004
6255
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
366
732
1098
1464
1830
<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:
0.228
Hom.:
586
Bravo
AF:
0.203
Asia WGS
AF:
0.371
AC:
1289
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
7.6
DANN
Benign
0.92
PhyloP100
0.065

Splicing

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

Publications

Other links and lift over

dbSNP: rs9288087; hg19: chr2-183732037; API