20-46869084-G-A

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 0.0928 in 152,110 control chromosomes in the GnomAD database, including 1,226 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 0.093 ( 1226 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.04
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 (EAS) allele frequency at 95% confidence interval = 0.417 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:
0.0928
AC:
14100
AN:
151992
Hom.:
1222
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0265
Gnomad AMI
AF:
0.0384
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.0678
Gnomad EAS
AF:
0.431
Gnomad SAS
AF:
0.147
Gnomad FIN
AF:
0.0925
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0777
Gnomad OTH
AF:
0.123
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0928
AC:
14113
AN:
152110
Hom.:
1226
Cov.:
32
AF XY:
0.0983
AC XY:
7309
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0264
Gnomad4 AMR
AF:
0.213
Gnomad4 ASJ
AF:
0.0678
Gnomad4 EAS
AF:
0.432
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.0925
Gnomad4 NFE
AF:
0.0777
Gnomad4 OTH
AF:
0.127
Alfa
AF:
0.0866
Hom.:
832
Bravo
AF:
0.104
Asia WGS
AF:
0.276
AC:
957
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
0.20
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: rs6124878; hg19: chr20-45497723; API