rs2833537

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 0.0809 in 151,732 control chromosomes in the GnomAD database, including 642 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 0.081 ( 642 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250
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 = 0.142 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:
0.0806
AC:
12225
AN:
151642
Hom.:
635
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.197
Gnomad AMR
AF:
0.0971
Gnomad ASJ
AF:
0.0496
Gnomad EAS
AF:
0.0952
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0626
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0378
Gnomad OTH
AF:
0.0740
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0809
AC:
12268
AN:
151732
Hom.:
642
Cov.:
32
AF XY:
0.0829
AC XY:
6148
AN XY:
74140
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.0978
Gnomad4 ASJ
AF:
0.0496
Gnomad4 EAS
AF:
0.0951
Gnomad4 SAS
AF:
0.110
Gnomad4 FIN
AF:
0.0626
Gnomad4 NFE
AF:
0.0378
Gnomad4 OTH
AF:
0.0748
Alfa
AF:
0.0565
Hom.:
101
Bravo
AF:
0.0864
Asia WGS
AF:
0.125
AC:
433
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.5
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: rs2833537; hg19: chr21-33213462; API