20-7869280-A-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 0.335 in 152,126 control chromosomes in the GnomAD database, including 13,916 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 0.33 ( 13916 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0920
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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:
0.334
AC:
50772
AN:
152008
Hom.:
13870
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.730
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.316
Gnomad ASJ
AF:
0.203
Gnomad EAS
AF:
0.563
Gnomad SAS
AF:
0.384
Gnomad FIN
AF:
0.0818
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.127
Gnomad OTH
AF:
0.318
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.335
AC:
50890
AN:
152126
Hom.:
13916
Cov.:
33
AF XY:
0.333
AC XY:
24785
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.316
Gnomad4 ASJ
AF:
0.203
Gnomad4 EAS
AF:
0.564
Gnomad4 SAS
AF:
0.385
Gnomad4 FIN
AF:
0.0818
Gnomad4 NFE
AF:
0.127
Gnomad4 OTH
AF:
0.322
Alfa
AF:
0.167
Hom.:
6198
Bravo
AF:
0.369
Asia WGS
AF:
0.503
AC:
1747
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.7
DANN
Benign
0.76

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: rs2205824; hg19: chr20-7849927; API