chr15-48737953-AGTTTATTTAAATAAGTTAACACTGCAGAGTGAGTCAATTTATAAGTATAAAAATAGATGGTTTAGAAACCAAAAATAAGCACCACACAAAAGCAGATTATACATACACCATCAGGCCTTTGGAATATTAAGGCAACATAAATATCTCAAGCAATTTTAGAAGAATGCTTTACTTATATAACAGATGTTATTAAAACATCTCAAAAGAGGCAGGGCTCACAATTTTTTTCAGTATGAGGTCTTCCCTTCCATTTTTGTTAATATATTAATGATTCTTCTTAAATACTGTACCATAATTAGTCTAGATTAACAAATGGGCTATCAAAGCCACTATCTTGTTGGCTAGATAGCGGAACAATTAATTTTCTTGAAGGCTGCTGACACACTGAAGATGGTAATGTACTGCTCAGTTTTTTGAAATCTGACTTTAATCTATCAGCCTTATGACGAGATGGGTGTCCACAATTCACACTGATCTTTCCTGGCTCCAAATACGTGGTTTCTTCTGACAGGTATGGAGTTTGATAACGCTGACATTTCATTGTTTGACAAATCATATTACTTTCCTCTGTATCTGAAAGATAACCGGATGGTGAAAACTGTTTGGATTTAACAGATTCACTTGGTATTTCCAAAGTTCCTTGTGGCCTACCATGTACAAATGATGCTTCACGACTGTCAAAGGATAAGGTTGCACTGCTGGAAGGCCAGCCCAAGCAGTCACTAAGGTCC-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001194998.2(CEP152):c.4698_*295del variant causes a stop lost, 3 prime UTR change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G1566G) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
CEP152
NM_001194998.2 stop_lost, 3_prime_UTR
NM_001194998.2 stop_lost, 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.95
Genes affected
CEP152 (HGNC:29298): (centrosomal protein 152) This gene encodes a protein that is thought to be involved with centrosome function. Mutations in this gene have been associated with primary microcephaly (MCPH4). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 15-48737953-AGTTTATTTAAATAAGTTAACACTGCAGAGTGAGTCAATTTATAAGTATAAAAATAGATGGTTTAGAAACCAAAAATAAGCACCACACAAAAGCAGATTATACATACACCATCAGGCCTTTGGAATATTAAGGCAACATAAATATCTCAAGCAATTTTAGAAGAATGCTTTACTTATATAACAGATGTTATTAAAACATCTCAAAAGAGGCAGGGCTCACAATTTTTTTCAGTATGAGGTCTTCCCTTCCATTTTTGTTAATATATTAATGATTCTTCTTAAATACTGTACCATAATTAGTCTAGATTAACAAATGGGCTATCAAAGCCACTATCTTGTTGGCTAGATAGCGGAACAATTAATTTTCTTGAAGGCTGCTGACACACTGAAGATGGTAATGTACTGCTCAGTTTTTTGAAATCTGACTTTAATCTATCAGCCTTATGACGAGATGGGTGTCCACAATTCACACTGATCTTTCCTGGCTCCAAATACGTGGTTTCTTCTGACAGGTATGGAGTTTGATAACGCTGACATTTCATTGTTTGACAAATCATATTACTTTCCTCTGTATCTGAAAGATAACCGGATGGTGAAAACTGTTTGGATTTAACAGATTCACTTGGTATTTCCAAAGTTCCTTGTGGCCTACCATGTACAAATGATGCTTCACGACTGTCAAAGGATAAGGTTGCACTGCTGGAAGGCCAGCCCAAGCAGTCACTAAGGTCC-A is Benign according to our data. Variant chr15-48737953-AGTTTATTTAAATAAGTTAACACTGCAGAGTGAGTCAATTTATAAGTATAAAAATAGATGGTTTAGAAACCAAAAATAAGCACCACACAAAAGCAGATTATACATACACCATCAGGCCTTTGGAATATTAAGGCAACATAAATATCTCAAGCAATTTTAGAAGAATGCTTTACTTATATAACAGATGTTATTAAAACATCTCAAAAGAGGCAGGGCTCACAATTTTTTTCAGTATGAGGTCTTCCCTTCCATTTTTGTTAATATATTAATGATTCTTCTTAAATACTGTACCATAATTAGTCTAGATTAACAAATGGGCTATCAAAGCCACTATCTTGTTGGCTAGATAGCGGAACAATTAATTTTCTTGAAGGCTGCTGACACACTGAAGATGGTAATGTACTGCTCAGTTTTTTGAAATCTGACTTTAATCTATCAGCCTTATGACGAGATGGGTGTCCACAATTCACACTGATCTTTCCTGGCTCCAAATACGTGGTTTCTTCTGACAGGTATGGAGTTTGATAACGCTGACATTTCATTGTTTGACAAATCATATTACTTTCCTCTGTATCTGAAAGATAACCGGATGGTGAAAACTGTTTGGATTTAACAGATTCACTTGGTATTTCCAAAGTTCCTTGTGGCCTACCATGTACAAATGATGCTTCACGACTGTCAAAGGATAAGGTTGCACTGCTGGAAGGCCAGCCCAAGCAGTCACTAAGGTCC-A is described in ClinVar as [Likely_benign]. Clinvar id is 2846165.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.4698_*295del | stop_lost, 3_prime_UTR_variant | 27/27 | ENST00000380950.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.4698_*295del | stop_lost, 3_prime_UTR_variant | 27/27 | 1 | NM_001194998.2 | A2 | ||
CEP152 | ENST00000399334.7 | coding_sequence_variant, 3_prime_UTR_variant | 26/26 | 1 | P2 | ||||
CEP152 | ENST00000561245.1 | c.142+2947_142+3677del | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 16, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.