chr20-51943113-T-C

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 0.631 in 152,022 control chromosomes in the GnomAD database, including 30,371 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 0.63 ( 30371 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306
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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.631
AC:
95909
AN:
151904
Hom.:
30342
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.615
Gnomad AMI
AF:
0.750
Gnomad AMR
AF:
0.665
Gnomad ASJ
AF:
0.719
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.626
Gnomad FIN
AF:
0.629
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.638
Gnomad OTH
AF:
0.652
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.631
AC:
95977
AN:
152022
Hom.:
30371
Cov.:
33
AF XY:
0.631
AC XY:
46846
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.615
Gnomad4 AMR
AF:
0.665
Gnomad4 ASJ
AF:
0.719
Gnomad4 EAS
AF:
0.491
Gnomad4 SAS
AF:
0.628
Gnomad4 FIN
AF:
0.629
Gnomad4 NFE
AF:
0.638
Gnomad4 OTH
AF:
0.655
Alfa
AF:
0.643
Hom.:
71511
Bravo
AF:
0.635
Asia WGS
AF:
0.573
AC:
1993
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.3
DANN
Benign
0.83

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: rs6068020; hg19: chr20-50559652; API