rs2839632
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000728699.1(ENSG00000295227):n.114-4225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00065 ( 1 hom., cov: 20)
Failed GnomAD Quality Control
Consequence
ENSG00000295227
ENST00000728699.1 intron
ENST00000728699.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.132
Publications
3 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
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 |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000295227 | ENST00000728699.1 | n.114-4225G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.000648 AC: 82AN: 126576Hom.: 1 Cov.: 20 show subpopulations
GnomAD3 genomes
AF:
AC:
82
AN:
126576
Hom.:
Cov.:
20
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000648 AC: 82AN: 126630Hom.: 1 Cov.: 20 AF XY: 0.000711 AC XY: 44AN XY: 61874 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
82
AN:
126630
Hom.:
Cov.:
20
AF XY:
AC XY:
44
AN XY:
61874
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
73
AN:
28532
American (AMR)
AF:
AC:
2
AN:
11562
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3114
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
1
AN:
4276
European-Finnish (FIN)
AF:
AC:
0
AN:
9746
Middle Eastern (MID)
AF:
AC:
0
AN:
234
European-Non Finnish (NFE)
AF:
AC:
5
AN:
61430
Other (OTH)
AF:
AC:
0
AN:
1696
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.273
Heterozygous variant carriers
0
8
16
25
33
41
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
548
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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