rs211833

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 0.529 in 152,130 control chromosomes in the GnomAD database, including 21,909 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 0.53 ( 21909 hom., cov: 34)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0560
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.529
AC:
80471
AN:
152012
Hom.:
21884
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.651
Gnomad AMI
AF:
0.461
Gnomad AMR
AF:
0.435
Gnomad ASJ
AF:
0.385
Gnomad EAS
AF:
0.410
Gnomad SAS
AF:
0.451
Gnomad FIN
AF:
0.566
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.457
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.529
AC:
80547
AN:
152130
Hom.:
21909
Cov.:
34
AF XY:
0.528
AC XY:
39266
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.650
Gnomad4 AMR
AF:
0.435
Gnomad4 ASJ
AF:
0.385
Gnomad4 EAS
AF:
0.411
Gnomad4 SAS
AF:
0.452
Gnomad4 FIN
AF:
0.566
Gnomad4 NFE
AF:
0.497
Gnomad4 OTH
AF:
0.460
Alfa
AF:
0.514
Hom.:
2394
Bravo
AF:
0.525
Asia WGS
AF:
0.468
AC:
1625
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.97
DANN
Benign
0.63

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: rs211833; hg19: chr20-38479281; API