chr22-46364179-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001378328.1(CELSR1):c.8852G>A(p.Arg2951Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,612,026 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2951W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378328.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.8852G>A | p.Arg2951Gln | missense_variant | 34/35 | ENST00000674500.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELSR1 | ENST00000674500.2 | c.8852G>A | p.Arg2951Gln | missense_variant | 34/35 | NM_001378328.1 | A2 | ||
CELSR1 | ENST00000262738.9 | c.8852G>A | p.Arg2951Gln | missense_variant | 34/35 | 1 | P4 | ||
CELSR1 | ENST00000473624.2 | c.605G>A | p.Arg202Gln | missense_variant | 5/5 | 1 | |||
CELSR1 | ENST00000674159.1 | n.2295G>A | non_coding_transcript_exon_variant | 10/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247352Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134534
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1459800Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 23AN XY: 726226
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2022 | The c.8852G>A (p.R2951Q) alteration is located in exon 34 (coding exon 34) of the CELSR1 gene. This alteration results from a G to A substitution at nucleotide position 8852, causing the arginine (R) at amino acid position 2951 to be replaced by a glutamine (Q). 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