rs854549

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 0.26 in 152,136 control chromosomes in the GnomAD database, including 5,902 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 0.26 ( 5902 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.458

Publications

9 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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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:
0.260
AC:
39507
AN:
152016
Hom.:
5901
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.141
Gnomad AMI
AF:
0.331
Gnomad AMR
AF:
0.253
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.0449
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.458
Gnomad NFE
AF:
0.341
Gnomad OTH
AF:
0.301
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.260
AC:
39512
AN:
152136
Hom.:
5902
Cov.:
32
AF XY:
0.254
AC XY:
18918
AN XY:
74358
show subpopulations
African (AFR)
AF:
0.141
AC:
5845
AN:
41512
American (AMR)
AF:
0.252
AC:
3856
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.408
AC:
1415
AN:
3472
East Asian (EAS)
AF:
0.0452
AC:
234
AN:
5178
South Asian (SAS)
AF:
0.212
AC:
1021
AN:
4818
European-Finnish (FIN)
AF:
0.276
AC:
2912
AN:
10566
Middle Eastern (MID)
AF:
0.469
AC:
136
AN:
290
European-Non Finnish (NFE)
AF:
0.341
AC:
23161
AN:
67992
Other (OTH)
AF:
0.298
AC:
630
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1458
2916
4375
5833
7291
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
408
816
1224
1632
2040
<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:
0.319
Hom.:
10353
Bravo
AF:
0.253
Asia WGS
AF:
0.120
AC:
420
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.5
DANN
Benign
0.69
PhyloP100
-0.46

Splicing

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

Publications

Other links and lift over

dbSNP: rs854549; hg19: chr7-94926585; API