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GeneBe

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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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