GeneBe

rs11269962

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 11600 hom., cov: 0)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.612

Publications

2 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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:
0.377
AC:
57271
AN:
151968
Hom.:
11602
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.456
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.522
Gnomad EAS
AF:
0.122
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.402
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.446
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.377
AC:
57288
AN:
152086
Hom.:
11600
Cov.:
0
AF XY:
0.372
AC XY:
27678
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.260
AC:
10783
AN:
41506
American (AMR)
AF:
0.404
AC:
6183
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.522
AC:
1811
AN:
3468
East Asian (EAS)
AF:
0.122
AC:
635
AN:
5188
South Asian (SAS)
AF:
0.396
AC:
1910
AN:
4820
European-Finnish (FIN)
AF:
0.402
AC:
4249
AN:
10578
Middle Eastern (MID)
AF:
0.500
AC:
147
AN:
294
European-Non Finnish (NFE)
AF:
0.446
AC:
30280
AN:
67924
Other (OTH)
AF:
0.415
AC:
876
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
1634
3268
4901
6535
8169
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
562
1124
1686
2248
2810
<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:
0.404
Hom.:
1550
Bravo
AF:
0.373
Asia WGS
AF:
0.236
AC:
822
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.61

Splicing

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

Publications

Other links and lift over

dbSNP: rs11269962; hg19: chr7-128575797; API