rs1592272

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 0.00991 in 152,314 control chromosomes in the GnomAD database, including 76 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 0.0099 ( 76 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

0 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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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:
0.00995
AC:
1514
AN:
152196
Hom.:
77
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00198
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0202
Gnomad ASJ
AF:
0.00375
Gnomad EAS
AF:
0.153
Gnomad SAS
AF:
0.0106
Gnomad FIN
AF:
0.0160
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00109
Gnomad OTH
AF:
0.0100
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00991
AC:
1510
AN:
152314
Hom.:
76
Cov.:
33
AF XY:
0.0114
AC XY:
852
AN XY:
74478
show subpopulations
African (AFR)
AF:
0.00197
AC:
82
AN:
41572
American (AMR)
AF:
0.0203
AC:
310
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
0.00375
AC:
13
AN:
3470
East Asian (EAS)
AF:
0.153
AC:
791
AN:
5180
South Asian (SAS)
AF:
0.0106
AC:
51
AN:
4826
European-Finnish (FIN)
AF:
0.0160
AC:
170
AN:
10612
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.00109
AC:
74
AN:
68028
Other (OTH)
AF:
0.00851
AC:
18
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
68
136
203
271
339
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
26
52
78
104
130
<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:
0.00348
Hom.:
4
Bravo
AF:
0.0122
Asia WGS
AF:
0.0570
AC:
199
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
0.50
DANN
Benign
0.44
PhyloP100
-1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs1592272; hg19: chr20-58054849; API