rs1187321

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 0.714 in 152,188 control chromosomes in the GnomAD database, including 40,219 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 0.71 ( 40219 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.477

Publications

6 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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 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:
0.714
AC:
108569
AN:
152070
Hom.:
40208
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.492
Gnomad AMI
AF:
0.886
Gnomad AMR
AF:
0.768
Gnomad ASJ
AF:
0.783
Gnomad EAS
AF:
0.788
Gnomad SAS
AF:
0.750
Gnomad FIN
AF:
0.835
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.803
Gnomad OTH
AF:
0.742
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.714
AC:
108634
AN:
152188
Hom.:
40219
Cov.:
33
AF XY:
0.717
AC XY:
53354
AN XY:
74404
show subpopulations
African (AFR)
AF:
0.493
AC:
20441
AN:
41494
American (AMR)
AF:
0.768
AC:
11748
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.783
AC:
2718
AN:
3472
East Asian (EAS)
AF:
0.789
AC:
4083
AN:
5178
South Asian (SAS)
AF:
0.751
AC:
3622
AN:
4826
European-Finnish (FIN)
AF:
0.835
AC:
8859
AN:
10606
Middle Eastern (MID)
AF:
0.718
AC:
211
AN:
294
European-Non Finnish (NFE)
AF:
0.803
AC:
54584
AN:
68000
Other (OTH)
AF:
0.740
AC:
1562
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1504
3008
4511
6015
7519
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
828
1656
2484
3312
4140
<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:
0.697
Hom.:
2277
Bravo
AF:
0.699
Asia WGS
AF:
0.727
AC:
2529
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
7.7
DANN
Benign
0.63
PhyloP100
0.48
PromoterAI
-0.0032
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1187321; hg19: chr9-87283031; API