20-50503858-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 0.516 in 151,984 control chromosomes in the GnomAD database, including 20,884 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 0.52 ( 20884 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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:
0.516
AC:
78323
AN:
151866
Hom.:
20848
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.658
Gnomad AMI
AF:
0.420
Gnomad AMR
AF:
0.488
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.300
Gnomad SAS
AF:
0.371
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.478
Gnomad OTH
AF:
0.489
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
78415
AN:
151984
Hom.:
20884
Cov.:
32
AF XY:
0.512
AC XY:
38047
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.659
Gnomad4 AMR
AF:
0.489
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.301
Gnomad4 SAS
AF:
0.370
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.478
Gnomad4 OTH
AF:
0.486
Alfa
AF:
0.483
Hom.:
8433
Bravo
AF:
0.526
Asia WGS
AF:
0.366
AC:
1274
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.29
DANN
Benign
0.54

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: rs6020563; hg19: chr20-49120395; API