rs1293470

Variant summary

Our verdict is Likely benign. The variant received -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 0.69 ( 19054 hom., 22372 hem., cov: 24)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16

Publications

2 publications found
Variant links:

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ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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:
0.686
AC:
76023
AN:
110895
Hom.:
19056
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.733
Gnomad AMI
AF:
0.810
Gnomad AMR
AF:
0.535
Gnomad ASJ
AF:
0.791
Gnomad EAS
AF:
0.228
Gnomad SAS
AF:
0.392
Gnomad FIN
AF:
0.678
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.726
Gnomad OTH
AF:
0.702
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:
0.686
AC:
76058
AN:
110948
Hom.:
19054
Cov.:
24
AF XY:
0.673
AC XY:
22372
AN XY:
33242
show subpopulations
African (AFR)
AF:
0.733
AC:
22413
AN:
30576
American (AMR)
AF:
0.534
AC:
5557
AN:
10397
Ashkenazi Jewish (ASJ)
AF:
0.791
AC:
2083
AN:
2632
East Asian (EAS)
AF:
0.228
AC:
802
AN:
3513
South Asian (SAS)
AF:
0.390
AC:
1050
AN:
2690
European-Finnish (FIN)
AF:
0.678
AC:
4017
AN:
5924
Middle Eastern (MID)
AF:
0.745
AC:
158
AN:
212
European-Non Finnish (NFE)
AF:
0.726
AC:
38367
AN:
52814
Other (OTH)
AF:
0.702
AC:
1062
AN:
1512
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
841
1682
2522
3363
4204
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
664
1328
1992
2656
3320
<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:
0.691
Hom.:
28895
Bravo
AF:
0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
7.0
DANN
Benign
0.78
PhyloP100
1.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs1293470; hg19: chrX-122211932; API