rs4779584

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 0.668 in 152,122 control chromosomes in the GnomAD database, including 36,462 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 0.67 ( 36462 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.204
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 (NFE) allele frequency at 95% confidence interval = 0.801 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:
0.668
AC:
101515
AN:
152004
Hom.:
36436
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.911
Gnomad AMR
AF:
0.733
Gnomad ASJ
AF:
0.874
Gnomad EAS
AF:
0.193
Gnomad SAS
AF:
0.593
Gnomad FIN
AF:
0.716
Gnomad MID
AF:
0.772
Gnomad NFE
AF:
0.807
Gnomad OTH
AF:
0.710
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.668
AC:
101591
AN:
152122
Hom.:
36462
Cov.:
33
AF XY:
0.663
AC XY:
49285
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.733
Gnomad4 ASJ
AF:
0.874
Gnomad4 EAS
AF:
0.194
Gnomad4 SAS
AF:
0.593
Gnomad4 FIN
AF:
0.716
Gnomad4 NFE
AF:
0.806
Gnomad4 OTH
AF:
0.707
Alfa
AF:
0.768
Hom.:
68934
Bravo
AF:
0.662
Asia WGS
AF:
0.419
AC:
1460
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.1
DANN
Benign
0.74

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: rs4779584; hg19: chr15-32994756; API