14-55482908-A-G

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 0.286 in 152,102 control chromosomes in the GnomAD database, including 7,357 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 0.29 ( 7357 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270

Publications

3 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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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:
0.286
AC:
43463
AN:
151984
Hom.:
7346
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.108
Gnomad AMI
AF:
0.238
Gnomad AMR
AF:
0.346
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.467
Gnomad SAS
AF:
0.486
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.313
Gnomad NFE
AF:
0.329
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43497
AN:
152102
Hom.:
7357
Cov.:
33
AF XY:
0.297
AC XY:
22063
AN XY:
74344
show subpopulations
African (AFR)
AF:
0.108
AC:
4475
AN:
41520
American (AMR)
AF:
0.346
AC:
5289
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.276
AC:
960
AN:
3472
East Asian (EAS)
AF:
0.467
AC:
2420
AN:
5180
South Asian (SAS)
AF:
0.485
AC:
2339
AN:
4820
European-Finnish (FIN)
AF:
0.447
AC:
4722
AN:
10558
Middle Eastern (MID)
AF:
0.320
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
0.329
AC:
22361
AN:
67964
Other (OTH)
AF:
0.293
AC:
620
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1489
2978
4466
5955
7444
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
452
904
1356
1808
2260
<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:
0.305
Hom.:
1401
Bravo
AF:
0.274
Asia WGS
AF:
0.479
AC:
1662
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
3.7
DANN
Benign
0.72
PhyloP100
-0.027

Splicing

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

Publications

Other links and lift over

dbSNP: rs12433615; hg19: chr14-55949626; API