1-109250083-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_001408.3(CELSR2):c.4C>T(p.Arg2Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000539 in 1,484,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001408.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELSR2 | NM_001408.3 | c.4C>T | p.Arg2Trp | missense_variant | 1/34 | ENST00000271332.4 | NP_001399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELSR2 | ENST00000271332.4 | c.4C>T | p.Arg2Trp | missense_variant | 1/34 | 1 | NM_001408.3 | ENSP00000271332.3 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151234Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000225 AC: 3AN: 1333522Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 659572
GnomAD4 genome AF: 0.0000331 AC: 5AN: 151234Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73826
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.4C>T (p.R2W) alteration is located in exon 1 (coding exon 1) of the CELSR2 gene. This alteration results from a C to T substitution at nucleotide position 4, causing the arginine (R) at amino acid position 2 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at