22-46390418-T-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001378328.1(CELSR1):c.6319A>T(p.Ile2107Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2107V) has been classified as Benign.
Frequency
Consequence
NM_001378328.1 missense
Scores
Clinical Significance
Conservation
Publications
- lymphatic malformation 9Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- neural tube defects, susceptibility toInheritance: AD Classification: MODERATE, LIMITED Submitted by: Illumina, Labcorp Genetics (formerly Invitae)
- epilepsyInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- hydrops fetalisInheritance: AD Classification: LIMITED Submitted by: G2P
- genetic developmental and epileptic encephalopathyInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.6319A>T | p.Ile2107Phe | missense_variant | Exon 17 of 35 | ENST00000674500.2 | NP_001365257.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELSR1 | ENST00000674500.2 | c.6319A>T | p.Ile2107Phe | missense_variant | Exon 17 of 35 | NM_001378328.1 | ENSP00000501367.2 | |||
CELSR1 | ENST00000262738.9 | c.6319A>T | p.Ile2107Phe | missense_variant | Exon 17 of 35 | 1 | ENSP00000262738.3 | |||
CELSR1 | ENST00000674341.1 | n.1396A>T | non_coding_transcript_exon_variant | Exon 9 of 19 | ||||||
CELSR1 | ENST00000674359.1 | c.*425A>T | downstream_gene_variant | ENSP00000501512.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.00000402 AC: 1AN: 248500 AF XY: 0.00 show subpopulations
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at