rs881333

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 0.709 in 152,070 control chromosomes in the GnomAD database, including 38,430 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 0.71 ( 38430 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158
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 (EAS) allele frequency at 95% confidence interval = 0.806 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:
0.709
AC:
107796
AN:
151952
Hom.:
38389
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.668
Gnomad AMI
AF:
0.794
Gnomad AMR
AF:
0.776
Gnomad ASJ
AF:
0.721
Gnomad EAS
AF:
0.827
Gnomad SAS
AF:
0.634
Gnomad FIN
AF:
0.742
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.709
Gnomad OTH
AF:
0.707
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.709
AC:
107882
AN:
152070
Hom.:
38430
Cov.:
31
AF XY:
0.714
AC XY:
53064
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.668
Gnomad4 AMR
AF:
0.776
Gnomad4 ASJ
AF:
0.721
Gnomad4 EAS
AF:
0.827
Gnomad4 SAS
AF:
0.634
Gnomad4 FIN
AF:
0.742
Gnomad4 NFE
AF:
0.709
Gnomad4 OTH
AF:
0.708
Alfa
AF:
0.668
Hom.:
2274
Bravo
AF:
0.709
Asia WGS
AF:
0.742
AC:
2581
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.7
DANN
Benign
0.46

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: rs881333; hg19: chr11-128740683; API