22-46364043-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001378328.1(CELSR1):āc.8988C>Gā(p.Ala2996Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00193 in 1,611,740 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001378328.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.8988C>G | p.Ala2996Ala | synonymous_variant | Exon 34 of 35 | ENST00000674500.2 | NP_001365257.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CELSR1 | ENST00000674500.2 | c.8988C>G | p.Ala2996Ala | synonymous_variant | Exon 34 of 35 | NM_001378328.1 | ENSP00000501367.2 | |||
CELSR1 | ENST00000262738.9 | c.8988C>G | p.Ala2996Ala | synonymous_variant | Exon 34 of 35 | 1 | ENSP00000262738.3 | |||
CELSR1 | ENST00000473624.2 | c.741C>G | p.Ala247Ala | synonymous_variant | Exon 5 of 5 | 1 | ENSP00000501353.1 | |||
CELSR1 | ENST00000674159.1 | n.2431C>G | non_coding_transcript_exon_variant | Exon 10 of 11 |
Frequencies
GnomAD3 genomes AF: 0.00823 AC: 1252AN: 152178Hom.: 18 Cov.: 33
GnomAD3 exomes AF: 0.00294 AC: 721AN: 245134Hom.: 10 AF XY: 0.00265 AC XY: 354AN XY: 133760
GnomAD4 exome AF: 0.00128 AC: 1867AN: 1459444Hom.: 38 Cov.: 31 AF XY: 0.00133 AC XY: 968AN XY: 725944
GnomAD4 genome AF: 0.00821 AC: 1251AN: 152296Hom.: 18 Cov.: 33 AF XY: 0.00794 AC XY: 591AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
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CELSR1-related disorder Benign:1
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