rs2828520

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 0.668 in 151,962 control chromosomes in the GnomAD database, including 34,271 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 0.67 ( 34271 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.94
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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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:
0.668
AC:
101499
AN:
151844
Hom.:
34238
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.762
Gnomad AMR
AF:
0.728
Gnomad ASJ
AF:
0.709
Gnomad EAS
AF:
0.862
Gnomad SAS
AF:
0.687
Gnomad FIN
AF:
0.733
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.671
Gnomad OTH
AF:
0.662
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.668
AC:
101575
AN:
151962
Hom.:
34271
Cov.:
32
AF XY:
0.675
AC XY:
50129
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.595
Gnomad4 AMR
AF:
0.729
Gnomad4 ASJ
AF:
0.709
Gnomad4 EAS
AF:
0.863
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.733
Gnomad4 NFE
AF:
0.671
Gnomad4 OTH
AF:
0.665
Alfa
AF:
0.673
Hom.:
79049
Bravo
AF:
0.667
Asia WGS
AF:
0.758
AC:
2635
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.25
DANN
Benign
0.35

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: rs2828520; hg19: chr21-25143119; API