20-50433551-C-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 0.65 in 151,948 control chromosomes in the GnomAD database, including 32,720 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 0.65 ( 32720 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.124
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=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 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:
0.651
AC:
98769
AN:
151830
Hom.:
32729
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.536
Gnomad AMI
AF:
0.616
Gnomad AMR
AF:
0.754
Gnomad ASJ
AF:
0.702
Gnomad EAS
AF:
0.536
Gnomad SAS
AF:
0.789
Gnomad FIN
AF:
0.758
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.676
Gnomad OTH
AF:
0.648
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.650
AC:
98787
AN:
151948
Hom.:
32720
Cov.:
31
AF XY:
0.658
AC XY:
48847
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.535
Gnomad4 AMR
AF:
0.755
Gnomad4 ASJ
AF:
0.702
Gnomad4 EAS
AF:
0.536
Gnomad4 SAS
AF:
0.788
Gnomad4 FIN
AF:
0.758
Gnomad4 NFE
AF:
0.676
Gnomad4 OTH
AF:
0.641
Alfa
AF:
0.545
Hom.:
1545
Bravo
AF:
0.645
Asia WGS
AF:
0.638
AC:
2221
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.6
DANN
Benign
0.29

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: rs2904268; hg19: chr20-49050088; API