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GeneBe

rs17300539

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0532 in 152,198 control chromosomes in the GnomAD database, including 327 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 0.053 ( 327 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.771
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0533
AC:
8099
AN:
152080
Hom.:
326
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0146
Gnomad AMI
AF:
0.0802
Gnomad AMR
AF:
0.0675
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0178
Gnomad FIN
AF:
0.0256
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0804
Gnomad OTH
AF:
0.0756
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0532
AC:
8094
AN:
152198
Hom.:
327
Cov.:
32
AF XY:
0.0510
AC XY:
3792
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0146
Gnomad4 AMR
AF:
0.0674
Gnomad4 ASJ
AF:
0.110
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0180
Gnomad4 FIN
AF:
0.0256
Gnomad4 NFE
AF:
0.0804
Gnomad4 OTH
AF:
0.0748
Alfa
AF:
0.0753
Hom.:
297
Bravo
AF:
0.0567
Asia WGS
AF:
0.0110
AC:
40
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
2.9
Dann
Benign
0.80

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17300539; hg19: chr3-186559460; API