19-23463609-G-A

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 0.475 in 151,960 control chromosomes in the GnomAD database, including 18,134 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 0.48 ( 18134 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

4 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 (EAS) allele frequency at 95% confidence interval = 0.812 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:
0.475
AC:
72101
AN:
151842
Hom.:
18098
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.486
Gnomad ASJ
AF:
0.392
Gnomad EAS
AF:
0.833
Gnomad SAS
AF:
0.447
Gnomad FIN
AF:
0.403
Gnomad MID
AF:
0.332
Gnomad NFE
AF:
0.390
Gnomad OTH
AF:
0.433
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.475
AC:
72185
AN:
151960
Hom.:
18134
Cov.:
32
AF XY:
0.477
AC XY:
35463
AN XY:
74280
show subpopulations
African (AFR)
AF:
0.599
AC:
24820
AN:
41418
American (AMR)
AF:
0.486
AC:
7434
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.392
AC:
1360
AN:
3466
East Asian (EAS)
AF:
0.833
AC:
4294
AN:
5156
South Asian (SAS)
AF:
0.447
AC:
2151
AN:
4816
European-Finnish (FIN)
AF:
0.403
AC:
4255
AN:
10564
Middle Eastern (MID)
AF:
0.327
AC:
96
AN:
294
European-Non Finnish (NFE)
AF:
0.390
AC:
26497
AN:
67936
Other (OTH)
AF:
0.430
AC:
910
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1856
3712
5567
7423
9279
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
646
1292
1938
2584
3230
<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:
0.404
Hom.:
4082
Bravo
AF:
0.487
Asia WGS
AF:
0.596
AC:
2073
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
1.4
DANN
Benign
0.61
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs584460; hg19: chr19-23646411; API