20-53652456-T-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 0.565 in 152,020 control chromosomes in the GnomAD database, including 26,242 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 0.57 ( 26242 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.456
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=-0.51).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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:
0.566
AC:
85938
AN:
151902
Hom.:
26246
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.323
Gnomad AMI
AF:
0.755
Gnomad AMR
AF:
0.562
Gnomad ASJ
AF:
0.656
Gnomad EAS
AF:
0.707
Gnomad SAS
AF:
0.492
Gnomad FIN
AF:
0.731
Gnomad MID
AF:
0.598
Gnomad NFE
AF:
0.675
Gnomad OTH
AF:
0.584
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.565
AC:
85946
AN:
152020
Hom.:
26242
Cov.:
33
AF XY:
0.568
AC XY:
42215
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.562
Gnomad4 ASJ
AF:
0.656
Gnomad4 EAS
AF:
0.708
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.731
Gnomad4 NFE
AF:
0.675
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.649
Hom.:
67859
Bravo
AF:
0.543
Asia WGS
AF:
0.573
AC:
1995
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
17
DANN
Benign
0.67

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: rs2041278; hg19: chr20-52268995; API