chr22-46364133-CGTGCGCGAGGAT-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 3P and 10B. PM4PP3BP6_ModerateBS1BS2
The NM_001378328.1(CELSR1):c.8886_8897delATCCTCGCGCAC(p.Ser2963_Thr2966del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,612,304 control chromosomes in the GnomAD database, including 33 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001378328.1 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.8886_8897delATCCTCGCGCAC | p.Ser2963_Thr2966del | disruptive_inframe_deletion | 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.8886_8897delATCCTCGCGCAC | p.Ser2963_Thr2966del | disruptive_inframe_deletion | Exon 34 of 35 | NM_001378328.1 | ENSP00000501367.2 | |||
CELSR1 | ENST00000262738.9 | c.8886_8897delATCCTCGCGCAC | p.Ser2963_Thr2966del | disruptive_inframe_deletion | Exon 34 of 35 | 1 | ENSP00000262738.3 | |||
CELSR1 | ENST00000473624.2 | c.639_650delATCCTCGCGCAC | p.Ser214_Thr217del | disruptive_inframe_deletion | Exon 5 of 5 | 1 | ENSP00000501353.1 | |||
CELSR1 | ENST00000674159.1 | n.2329_2340delATCCTCGCGCAC | non_coding_transcript_exon_variant | Exon 10 of 11 |
Frequencies
GnomAD3 genomes AF: 0.00805 AC: 1225AN: 152228Hom.: 20 Cov.: 33
GnomAD3 exomes AF: 0.00203 AC: 504AN: 248514Hom.: 7 AF XY: 0.00149 AC XY: 201AN XY: 135070
GnomAD4 exome AF: 0.000801 AC: 1169AN: 1459958Hom.: 13 AF XY: 0.000625 AC XY: 454AN XY: 726260
GnomAD4 genome AF: 0.00804 AC: 1225AN: 152346Hom.: 20 Cov.: 33 AF XY: 0.00785 AC XY: 585AN XY: 74504
ClinVar
Submissions by phenotype
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at