chr13-47029825-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 0.0452 in 152,216 control chromosomes in the GnomAD database, including 222 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 0.045 ( 222 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.26

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 (AMR) allele frequency at 95% confidence interval = 0.0875 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:
0.0451
AC:
6866
AN:
152098
Hom.:
222
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0121
Gnomad AMI
AF:
0.0625
Gnomad AMR
AF:
0.0910
Gnomad ASJ
AF:
0.0196
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0215
Gnomad FIN
AF:
0.0486
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0611
Gnomad OTH
AF:
0.0372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0452
AC:
6876
AN:
152216
Hom.:
222
Cov.:
32
AF XY:
0.0440
AC XY:
3275
AN XY:
74410
show subpopulations
African (AFR)
AF:
0.0120
AC:
500
AN:
41542
American (AMR)
AF:
0.0914
AC:
1398
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.0196
AC:
68
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5166
South Asian (SAS)
AF:
0.0218
AC:
105
AN:
4826
European-Finnish (FIN)
AF:
0.0486
AC:
515
AN:
10604
Middle Eastern (MID)
AF:
0.00340
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
0.0611
AC:
4154
AN:
67996
Other (OTH)
AF:
0.0369
AC:
78
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
347
694
1040
1387
1734
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
70
140
210
280
350
<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:
0.0610
Hom.:
123
Bravo
AF:
0.0460
Asia WGS
AF:
0.0150
AC:
53
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
1.9
DANN
Benign
0.68
PhyloP100
-2.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs12860002; hg19: chr13-47603960; API