rs6007897
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378328.1(CELSR1):āc.6802A>Gā(p.Thr2268Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,613,128 control chromosomes in the GnomAD database, including 32,578 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T2268S) has been classified as Benign.
Frequency
Consequence
NM_001378328.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELSR1 | NM_001378328.1 | c.6802A>G | p.Thr2268Ala | missense_variant | 20/35 | ENST00000674500.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELSR1 | ENST00000674500.2 | c.6802A>G | p.Thr2268Ala | missense_variant | 20/35 | NM_001378328.1 | A2 | ||
CELSR1 | ENST00000262738.9 | c.6802A>G | p.Thr2268Ala | missense_variant | 20/35 | 1 | P4 | ||
CELSR1 | ENST00000674341.1 | n.1879A>G | non_coding_transcript_exon_variant | 12/19 | |||||
CELSR1 | ENST00000674379.1 | n.159A>G | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.267 AC: 40599AN: 151946Hom.: 8345 Cov.: 32
GnomAD3 exomes AF: 0.157 AC: 39241AN: 250544Hom.: 5050 AF XY: 0.149 AC XY: 20177AN XY: 135466
GnomAD4 exome AF: 0.164 AC: 239577AN: 1461064Hom.: 24202 Cov.: 32 AF XY: 0.161 AC XY: 116799AN XY: 726818
GnomAD4 genome ? AF: 0.267 AC: 40674AN: 152064Hom.: 8376 Cov.: 32 AF XY: 0.259 AC XY: 19242AN XY: 74352
ClinVar
Submissions by phenotype
CELSR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2019 | 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