rs17148729

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 0.298 in 151,716 control chromosomes in the GnomAD database, including 6,997 homozygotes. There are 21,944 hemizygotes in GnomAD. 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 0.30 ( 6997 hom., 21944 hem., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

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=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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:
0.299
AC:
45254
AN:
151596
Hom.:
7005
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.243
Gnomad AMI
AF:
0.268
Gnomad AMR
AF:
0.316
Gnomad ASJ
AF:
0.342
Gnomad EAS
AF:
0.341
Gnomad SAS
AF:
0.349
Gnomad FIN
AF:
0.256
Gnomad MID
AF:
0.433
Gnomad NFE
AF:
0.326
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45256
AN:
151716
Hom.:
6997
Cov.:
30
AF XY:
0.296
AC XY:
21944
AN XY:
74108
show subpopulations
African (AFR)
AF:
0.243
AC:
10051
AN:
41404
American (AMR)
AF:
0.316
AC:
4800
AN:
15210
Ashkenazi Jewish (ASJ)
AF:
0.342
AC:
1185
AN:
3460
East Asian (EAS)
AF:
0.342
AC:
1751
AN:
5122
South Asian (SAS)
AF:
0.348
AC:
1666
AN:
4788
European-Finnish (FIN)
AF:
0.256
AC:
2697
AN:
10544
Middle Eastern (MID)
AF:
0.435
AC:
128
AN:
294
European-Non Finnish (NFE)
AF:
0.326
AC:
22097
AN:
67878
Other (OTH)
AF:
0.303
AC:
638
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1562
3124
4687
6249
7811
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
468
936
1404
1872
2340
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Bravo
AF:
0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.4
DANN
Benign
0.17
PhyloP100
0.036

Splicing

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

Publications

Other links and lift over

dbSNP: rs17148729; hg19: chrX-818949; API