19-10025011-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 0.799 in 151,872 control chromosomes in the GnomAD database, including 49,092 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 0.80 ( 49092 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.515

Publications

8 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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 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:
0.798
AC:
121167
AN:
151756
Hom.:
49037
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.921
Gnomad AMI
AF:
0.719
Gnomad AMR
AF:
0.771
Gnomad ASJ
AF:
0.696
Gnomad EAS
AF:
0.503
Gnomad SAS
AF:
0.774
Gnomad FIN
AF:
0.822
Gnomad MID
AF:
0.758
Gnomad NFE
AF:
0.757
Gnomad OTH
AF:
0.783
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.799
AC:
121278
AN:
151872
Hom.:
49092
Cov.:
32
AF XY:
0.799
AC XY:
59275
AN XY:
74196
show subpopulations
African (AFR)
AF:
0.921
AC:
38211
AN:
41492
American (AMR)
AF:
0.770
AC:
11760
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.696
AC:
2410
AN:
3462
East Asian (EAS)
AF:
0.504
AC:
2594
AN:
5148
South Asian (SAS)
AF:
0.774
AC:
3739
AN:
4828
European-Finnish (FIN)
AF:
0.822
AC:
8610
AN:
10470
Middle Eastern (MID)
AF:
0.760
AC:
222
AN:
292
European-Non Finnish (NFE)
AF:
0.757
AC:
51423
AN:
67894
Other (OTH)
AF:
0.784
AC:
1656
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1221
2442
3662
4883
6104
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
862
1724
2586
3448
4310
<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:
0.762
Hom.:
70006
Bravo
AF:
0.796
Asia WGS
AF:
0.726
AC:
2526
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.77
DANN
Benign
0.84
PhyloP100
-0.52

Splicing

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

Publications

Other links and lift over

dbSNP: rs1673130; hg19: chr19-10135687; API