rs1933752

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 0.348 in 152,116 control chromosomes in the GnomAD database, including 10,299 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 0.35 ( 10299 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.302

Publications

2 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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:
0.348
AC:
52868
AN:
151998
Hom.:
10271
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.236
Gnomad AMR
AF:
0.489
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.753
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.215
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.264
Gnomad OTH
AF:
0.361
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.348
AC:
52942
AN:
152116
Hom.:
10299
Cov.:
33
AF XY:
0.354
AC XY:
26288
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.412
AC:
17094
AN:
41508
American (AMR)
AF:
0.490
AC:
7488
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.294
AC:
1020
AN:
3472
East Asian (EAS)
AF:
0.753
AC:
3880
AN:
5152
South Asian (SAS)
AF:
0.438
AC:
2111
AN:
4818
European-Finnish (FIN)
AF:
0.215
AC:
2272
AN:
10586
Middle Eastern (MID)
AF:
0.405
AC:
119
AN:
294
European-Non Finnish (NFE)
AF:
0.264
AC:
17972
AN:
67972
Other (OTH)
AF:
0.365
AC:
771
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1724
3449
5173
6898
8622
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
514
1028
1542
2056
2570
<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:
0.285
Hom.:
3569
Bravo
AF:
0.372
Asia WGS
AF:
0.568
AC:
1975
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.4
DANN
Benign
0.76
PhyloP100
0.30

Splicing

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

Publications

Other links and lift over

dbSNP: rs1933752; hg19: chr6-145185269; API