NM_018451.5:c.1881G>A
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_018451.5(CPAP):c.1881G>A(p.Pro627Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,606 control chromosomes in the GnomAD database, including 1,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018451.5 synonymous
Scores
Clinical Significance
Conservation
Publications
- microcephaly 6 with or without short statureInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- microcephaly 6, primary, autosomal recessiveInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- autosomal recessive primary microcephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Seckel syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPJ | ENST00000381884.9 | c.1881G>A | p.Pro627Pro | synonymous_variant | Exon 7 of 17 | 1 | NM_018451.5 | ENSP00000371308.4 | ||
CENPJ | ENST00000616936.4 | n.1881G>A | non_coding_transcript_exon_variant | Exon 7 of 16 | 1 | ENSP00000477511.1 | ||||
CENPJ | ENST00000545981.6 | n.1881G>A | non_coding_transcript_exon_variant | Exon 7 of 18 | 2 | ENSP00000441090.2 |
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2748AN: 152080Hom.: 194 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0371 AC: 9325AN: 251226 AF XY: 0.0291 show subpopulations
GnomAD4 exome AF: 0.0100 AC: 14645AN: 1461408Hom.: 1264 Cov.: 34 AF XY: 0.00897 AC XY: 6517AN XY: 726900 show subpopulations
GnomAD4 genome AF: 0.0181 AC: 2761AN: 152198Hom.: 199 Cov.: 33 AF XY: 0.0217 AC XY: 1614AN XY: 74412 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
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Seckel syndrome 4 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Microcephaly 6, primary, autosomal recessive Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at