18-51463692-C-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

0 publications found
Variant links:
Genes affected
LINC01630 (HGNC:52295): (long intergenic non-protein coding RNA 1630)

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC01630NR_040074.1 linkn.216+71435C>A intron_variant Intron 1 of 2
LINC01630NR_040075.1 linkn.217-1715C>A intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01630ENST00000435144.7 linkn.219+71435C>A intron_variant Intron 1 of 6 5
LINC01630ENST00000578152.5 linkn.217-1715C>A intron_variant Intron 1 of 1 2
LINC01630ENST00000580841.1 linkn.216+71435C>A intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.00000730
AC:
1
AN:
136928
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000231
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
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:
1
AN:
137016
Hom.:
0
Cov.:
32
AF XY:
0.00
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:
0.00
AC:
0
AN:
36898
American (AMR)
AF:
0.00
AC:
0
AN:
13884
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3256
East Asian (EAS)
AF:
0.000231
AC:
1
AN:
4324
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3930
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9158
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
206
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
62628
Other (OTH)
AF:
0.00
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 in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.60
DANN
Benign
0.47
PhyloP100
-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs321834; hg19: chr18-48990062; API