20-51161341-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 0.803 in 152,120 control chromosomes in the GnomAD database, including 49,479 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 ( 49479 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.542
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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:
0.803
AC:
121986
AN:
152002
Hom.:
49428
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.925
Gnomad AMI
AF:
0.964
Gnomad AMR
AF:
0.743
Gnomad ASJ
AF:
0.776
Gnomad EAS
AF:
0.656
Gnomad SAS
AF:
0.627
Gnomad FIN
AF:
0.756
Gnomad MID
AF:
0.816
Gnomad NFE
AF:
0.772
Gnomad OTH
AF:
0.784
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.803
AC:
122093
AN:
152120
Hom.:
49479
Cov.:
32
AF XY:
0.797
AC XY:
59243
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.925
Gnomad4 AMR
AF:
0.743
Gnomad4 ASJ
AF:
0.776
Gnomad4 EAS
AF:
0.656
Gnomad4 SAS
AF:
0.627
Gnomad4 FIN
AF:
0.756
Gnomad4 NFE
AF:
0.772
Gnomad4 OTH
AF:
0.784
Alfa
AF:
0.775
Hom.:
11059
Bravo
AF:
0.810
Asia WGS
AF:
0.666
AC:
2318
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.50

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: rs2143630; hg19: chr20-49777878; API