22-46364165-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001378328.1(CELSR1):c.8866G>A(p.Asp2956Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,612,200 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_001378328.1 missense
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.8866G>A | p.Asp2956Asn | missense_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.8866G>A | p.Asp2956Asn | missense_variant | Exon 34 of 35 | NM_001378328.1 | ENSP00000501367.2 | |||
CELSR1 | ENST00000262738.9 | c.8866G>A | p.Asp2956Asn | missense_variant | Exon 34 of 35 | 1 | ENSP00000262738.3 | |||
CELSR1 | ENST00000473624.2 | c.619G>A | p.Asp207Asn | missense_variant | Exon 5 of 5 | 1 | ENSP00000501353.1 | |||
CELSR1 | ENST00000674159.1 | n.2309G>A | non_coding_transcript_exon_variant | Exon 10 of 11 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248038Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134808
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459936Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726278
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.8866G>A (p.D2956N) 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 8866, causing the aspartic acid (D) at amino acid position 2956 to be replaced by an asparagine (N). 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