19-20716478-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.481 in 152,096 control chromosomes in the GnomAD database, including 17,904 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 ( 17904 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.06).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 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:
0.481
AC:
73149
AN:
151978
Hom.:
17885
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.448
Gnomad AMI
AF:
0.569
Gnomad AMR
AF:
0.483
Gnomad ASJ
AF:
0.494
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.510
Gnomad FIN
AF:
0.468
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.517
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.481
AC:
73202
AN:
152096
Hom.:
17904
Cov.:
33
AF XY:
0.478
AC XY:
35518
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.448
Gnomad4 AMR
AF:
0.484
Gnomad4 ASJ
AF:
0.494
Gnomad4 EAS
AF:
0.238
Gnomad4 SAS
AF:
0.510
Gnomad4 FIN
AF:
0.468
Gnomad4 NFE
AF:
0.517
Gnomad4 OTH
AF:
0.486
Alfa
AF:
0.501
Hom.:
4876
Bravo
AF:
0.479
Asia WGS
AF:
0.390
AC:
1357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
2.0
DANN
Benign
0.19

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7258003; hg19: chr19-20899284; API