rs1447537

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 0.386 in 151,928 control chromosomes in the GnomAD database, including 13,449 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 0.39 ( 13449 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.984

Publications

14 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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 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:
0.385
AC:
58516
AN:
151810
Hom.:
13401
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.606
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.224
Gnomad EAS
AF:
0.597
Gnomad SAS
AF:
0.247
Gnomad FIN
AF:
0.342
Gnomad MID
AF:
0.248
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.386
AC:
58620
AN:
151928
Hom.:
13449
Cov.:
32
AF XY:
0.390
AC XY:
28963
AN XY:
74262
show subpopulations
African (AFR)
AF:
0.606
AC:
25126
AN:
41436
American (AMR)
AF:
0.444
AC:
6773
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.224
AC:
776
AN:
3464
East Asian (EAS)
AF:
0.596
AC:
3077
AN:
5162
South Asian (SAS)
AF:
0.247
AC:
1187
AN:
4806
European-Finnish (FIN)
AF:
0.342
AC:
3607
AN:
10546
Middle Eastern (MID)
AF:
0.250
AC:
73
AN:
292
European-Non Finnish (NFE)
AF:
0.251
AC:
17061
AN:
67944
Other (OTH)
AF:
0.366
AC:
768
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1662
3324
4987
6649
8311
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
524
1048
1572
2096
2620
<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:
0.295
Hom.:
26204
Bravo
AF:
0.408
Asia WGS
AF:
0.413
AC:
1436
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.78
DANN
Benign
0.13
PhyloP100
-0.98

Splicing

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

Publications

Other links and lift over

dbSNP: rs1447537; hg19: chr2-84246586; API