rs4733263

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 0.551 in 151,814 control chromosomes in the GnomAD database, including 23,609 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 0.55 ( 23609 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.721
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=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 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:
0.551
AC:
83575
AN:
151698
Hom.:
23599
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.433
Gnomad AMI
AF:
0.623
Gnomad AMR
AF:
0.634
Gnomad ASJ
AF:
0.521
Gnomad EAS
AF:
0.421
Gnomad SAS
AF:
0.505
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.612
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.551
AC:
83606
AN:
151814
Hom.:
23609
Cov.:
32
AF XY:
0.551
AC XY:
40853
AN XY:
74194
show subpopulations
Gnomad4 AFR
AF:
0.432
Gnomad4 AMR
AF:
0.634
Gnomad4 ASJ
AF:
0.521
Gnomad4 EAS
AF:
0.420
Gnomad4 SAS
AF:
0.505
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.612
Gnomad4 OTH
AF:
0.535
Alfa
AF:
0.597
Hom.:
55324
Bravo
AF:
0.548
Asia WGS
AF:
0.503
AC:
1739
AN:
3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
7.1
DANN
Benign
0.20

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: rs4733263; hg19: chr8-31490474; API