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GeneBe

rs5929706

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.98 ( 37755 hom., 32271 hem., cov: 23)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20
Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.06).

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:
0.00
AC:
108851
AN:
110505
Hom.:
37759
Cov.:
23
AF XY:
0.986
AC XY:
32216
AN XY:
32683
FAILED QC
Gnomad AFR
AF:
0.949
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.995
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
0.999
Gnomad OTH
AF:
0.982
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.985
AC:
108898
AN:
110558
Hom.:
37755
Cov.:
23
AF XY:
0.985
AC XY:
32271
AN XY:
32746
show subpopulations
Gnomad4 AFR
AF:
0.949
Gnomad4 AMR
AF:
0.995
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.999
Gnomad4 OTH
AF:
0.983
Alfa
AF:
0.991
Hom.:
10484
Bravo
AF:
0.983

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
Cadd
Benign
0.78
Dann
Benign
0.38

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: rs5929706; hg19: chrX-135017531; API