chr22-46364140-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378328.1(CELSR1):c.8891C>T(p.Ser2964Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,607,994 control chromosomes in the GnomAD database, including 280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S2964S) has been classified as Likely benign.
Frequency
Consequence
NM_001378328.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.8891C>T | p.Ser2964Leu | missense_variant | 34/35 | ENST00000674500.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELSR1 | ENST00000674500.2 | c.8891C>T | p.Ser2964Leu | missense_variant | 34/35 | NM_001378328.1 | A2 | ||
CELSR1 | ENST00000262738.9 | c.8891C>T | p.Ser2964Leu | missense_variant | 34/35 | 1 | P4 | ||
CELSR1 | ENST00000473624.2 | c.644C>T | p.Ser215Leu | missense_variant | 5/5 | 1 | |||
CELSR1 | ENST00000674159.1 | n.2334C>T | non_coding_transcript_exon_variant | 10/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0240 AC: 3603AN: 150012Hom.: 139 Cov.: 33
GnomAD3 exomes AF: 0.00594 AC: 1477AN: 248558Hom.: 63 AF XY: 0.00406 AC XY: 548AN XY: 135070
GnomAD4 exome AF: 0.00244 AC: 3553AN: 1457866Hom.: 141 Cov.: 31 AF XY: 0.00209 AC XY: 1514AN XY: 725432
GnomAD4 genome ? AF: 0.0240 AC: 3608AN: 150128Hom.: 139 Cov.: 33 AF XY: 0.0228 AC XY: 1677AN XY: 73440
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 21, 2020 | This variant is associated with the following publications: (PMID: 22095531) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
CELSR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at