Variant 15-48737953-AGTTTATTTAAATAAGTTAACACTGCAGAGTGAGTCAATTTATAAGTATAAAAATAGATGGTTTAGAAACCAAAAATAAGCACCACACAAAAGCAGATTATACATACACCATCAGGCCTTTGGAATATTAAGGCAACATAAATATCTCAAGCAATTTTAGAAGAATGCTTTACTTATATAACAGATGTTATTAAAACATCTCAAAAGAGGCAGGGCTCACAATTTTTTTCAGTATGAGGTCTTCCCTTCCATTTTTGTTAATATATTAATGATTCTTCTTAAATACTGTACCATAATTAGTCTAGATTAACAAATGGGCTATCAAAGCCACTATCTTGTTGGCTAGATAGCGGAACAATTAATTTTCTTGAAGGCTGCTGACACACTGAAGATGGTAATGTACTGCTCAGTTTTTTGAAATCTGACTTTAATCTATCAGCCTTATGACGAGATGGGTGTCCACAATTCACACTGATCTTTCCTGGCTCCAAATACGTGGTTTCTTCTGACAGGTATGGAGTTTGATAACGCTGACATTTCATTGTTTGACAAATCATATTACTTTCCTCTGTATCTGAAAGATAACCGGATGGTGAAAACTGTTTGGATTTAACAGATTCACTTGGTATTTCCAAAGTTCCTTGTGGCCTACCATGTACAAATGATGCTTCACGACTGTCAAAGGATAAGGTTGCACTGCTGGAAGGCCAGCCCAAGCAGTCACTAAGGTCC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 10P and 2B. PVS1PM2BP6_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 (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CEP152
NM_001194998.2 stop_lost, 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.95

Variant links:

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]

CEP152 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PVS1

Stoplost variant. No alternative stopcodon identified downstream, so we assume a Nonstop Mediated Decay. LoF is a known mechanism of disease.

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	Protein	UniProt
CEP152	NM_001194998.2 linkuse as main transcript	c.4698_*295del		stop_lost, 3_prime_UTR_variant	27/27	ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7 linkuse as main transcript	c.4698_*295del	stop_lost, 3_prime_UTR_variant	27/27	1	NM_001194998.2	ENSP00000370337	A2	O94986-4
CEP152	ENST00000399334.7 linkuse as main transcript		coding_sequence_variant, 3_prime_UTR_variant	26/26	1		ENSP00000382271	P2	O94986-3
CEP152	ENST00000561245.1 linkuse as main transcript	c.142+2947_142+3677del	intron_variant, NMD_transcript_variant		2		ENSP00000453591

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

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

Labcorp Genetics (formerly Invitae), Labcorp

Mar 16, 2023

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.