15-100569122-CAAAAAA-C
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001040616.3(LINS1):c.*110_*115delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000189 in 371,298 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000019 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LINS1
NM_001040616.3 3_prime_UTR
NM_001040616.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.37
Publications
0 publications found
Genes affected
LINS1 (HGNC:30922): (lines homolog 1) The Drosophila segment polarity gene lin encodes a protein, lines, which plays important roles in development of the epidermis and hindgut. This gene encodes a protein containing a lines-like domain. This gene is located on chromosome 15 and clustered with the gene encoding ankyrin repeat and SOCS box-containing protein 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]
LINS1 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- intellectual disability, autosomal recessive 27Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- autosomal recessive non-syndromic intellectual disabilityInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINS1 | ENST00000314742.13 | c.*110_*115delTTTTTT | 3_prime_UTR_variant | Exon 7 of 7 | 5 | NM_001040616.3 | ENSP00000318423.8 | |||
LINS1 | ENST00000560783.1 | n.191-3863_191-3858delTTTTTT | intron_variant | Intron 1 of 3 | 5 | ENSP00000474128.1 | ||||
LINS1 | ENST00000559169.1 | n.*107_*112delTTTTTT | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 106108Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
106108
Hom.:
Cov.:
0
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:
GnomAD4 exome AF: 0.0000189 AC: 7AN: 371298Hom.: 0 AF XY: 0.0000306 AC XY: 6AN XY: 196032 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
7
AN:
371298
Hom.:
AF XY:
AC XY:
6
AN XY:
196032
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
10602
American (AMR)
AF:
AC:
1
AN:
14712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10748
East Asian (EAS)
AF:
AC:
1
AN:
25408
South Asian (SAS)
AF:
AC:
0
AN:
37456
European-Finnish (FIN)
AF:
AC:
0
AN:
20292
Middle Eastern (MID)
AF:
AC:
0
AN:
1514
European-Non Finnish (NFE)
AF:
AC:
2
AN:
230132
Other (OTH)
AF:
AC:
2
AN:
20434
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 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: 0.239
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 106108Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 48624
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
106108
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
48624
African (AFR)
AF:
AC:
0
AN:
27544
American (AMR)
AF:
AC:
0
AN:
9288
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2882
East Asian (EAS)
AF:
AC:
0
AN:
2986
South Asian (SAS)
AF:
AC:
0
AN:
2972
European-Finnish (FIN)
AF:
AC:
0
AN:
3028
Middle Eastern (MID)
AF:
AC:
0
AN:
210
European-Non Finnish (NFE)
AF:
AC:
0
AN:
55056
Other (OTH)
AF:
AC:
0
AN:
1342
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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