rs4864029

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 0.854 in 151,802 control chromosomes in the GnomAD database, including 55,850 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 0.85 ( 55850 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107
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=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.907 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:
0.855
AC:
129646
AN:
151694
Hom.:
55839
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.742
Gnomad AMI
AF:
0.910
Gnomad AMR
AF:
0.920
Gnomad ASJ
AF:
0.936
Gnomad EAS
AF:
0.867
Gnomad SAS
AF:
0.873
Gnomad FIN
AF:
0.815
Gnomad MID
AF:
0.934
Gnomad NFE
AF:
0.906
Gnomad OTH
AF:
0.877
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.854
AC:
129701
AN:
151802
Hom.:
55850
Cov.:
30
AF XY:
0.852
AC XY:
63182
AN XY:
74146
show subpopulations
Gnomad4 AFR
AF:
0.741
Gnomad4 AMR
AF:
0.920
Gnomad4 ASJ
AF:
0.936
Gnomad4 EAS
AF:
0.867
Gnomad4 SAS
AF:
0.873
Gnomad4 FIN
AF:
0.815
Gnomad4 NFE
AF:
0.906
Gnomad4 OTH
AF:
0.878
Alfa
AF:
0.901
Hom.:
83944
Bravo
AF:
0.857
Asia WGS
AF:
0.876
AC:
3047
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
1.9
DANN
Benign
0.15

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: rs4864029; hg19: chr4-132024484; API