rs7246355

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 0.524 in 151,918 control chromosomes in the GnomAD database, including 21,058 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 0.52 ( 21058 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0930

Publications

9 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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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:
0.524
AC:
79505
AN:
151800
Hom.:
21056
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.558
Gnomad AMI
AF:
0.612
Gnomad AMR
AF:
0.510
Gnomad ASJ
AF:
0.525
Gnomad EAS
AF:
0.391
Gnomad SAS
AF:
0.498
Gnomad FIN
AF:
0.556
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.512
Gnomad OTH
AF:
0.513
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.524
AC:
79547
AN:
151918
Hom.:
21058
Cov.:
31
AF XY:
0.524
AC XY:
38937
AN XY:
74258
show subpopulations
African (AFR)
AF:
0.558
AC:
23115
AN:
41424
American (AMR)
AF:
0.510
AC:
7784
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.525
AC:
1819
AN:
3466
East Asian (EAS)
AF:
0.390
AC:
2004
AN:
5138
South Asian (SAS)
AF:
0.499
AC:
2399
AN:
4808
European-Finnish (FIN)
AF:
0.556
AC:
5864
AN:
10548
Middle Eastern (MID)
AF:
0.493
AC:
145
AN:
294
European-Non Finnish (NFE)
AF:
0.512
AC:
34774
AN:
67950
Other (OTH)
AF:
0.513
AC:
1085
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1944
3889
5833
7778
9722
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
696
1392
2088
2784
3480
<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:
0.509
Hom.:
10171
Bravo
AF:
0.524
Asia WGS
AF:
0.465
AC:
1620
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.0
DANN
Benign
0.85
PhyloP100
-0.093
PromoterAI
0.017
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs7246355; hg19: chr19-51226244; API