18-51463692-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000435144.7(LINC01630):n.219+71435C>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 0.0000073 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
LINC01630
ENST00000435144.7 intron
ENST00000435144.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.28
Publications
0 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=-1.0).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC01630 | ENST00000435144.7 | n.219+71435C>A | intron_variant | Intron 1 of 6 | 5 | |||||
LINC01630 | ENST00000578152.5 | n.217-1715C>A | intron_variant | Intron 1 of 1 | 2 | |||||
LINC01630 | ENST00000580841.1 | n.216+71435C>A | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000730 AC: 1AN: 136928Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
136928
Hom.:
Cov.:
32
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: 0.00000730 AC: 1AN: 137016Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 67004 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:
1
AN:
137016
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
67004
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
36898
American (AMR)
AF:
AC:
0
AN:
13884
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3256
East Asian (EAS)
AF:
AC:
1
AN:
4324
South Asian (SAS)
AF:
AC:
0
AN:
3930
European-Finnish (FIN)
AF:
AC:
0
AN:
9158
Middle Eastern (MID)
AF:
AC:
0
AN:
206
European-Non Finnish (NFE)
AF:
AC:
0
AN:
62628
Other (OTH)
AF:
AC:
0
AN:
1914
⚠️ 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: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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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