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GeneBe

rs4420638

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 0.18 in 151670 control chromosomes in the gnomAD Genomes database, including 2557 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.18 ( 2557 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -1.31

Links

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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:
0.180
AC:
27280
AN:
151670
Hom.:
2557
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.197
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.150
Gnomad EAS
AF:
0.113
Gnomad SAS
AF:
0.131
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.143
Gnomad NFE
AF:
0.175
Gnomad OTH
AF:
0.139
Alfa
AF:
0.169
Hom.:
1920
Bravo
AF:
0.168
Asia WGS
AF:
0.180
AC:
627
AN:
3478

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
not provided, no classification providednot providedDepartment of Ophthalmology and Visual Sciences Kyoto University-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.27
Dann
Benign
0.59

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: rs4420638; hg19: chr19-45422946; API