15-48737953-AGTTTATTTAAATAAGTTAACACTGCAGAGTGAGTCAATTTATAAGTATAAAAATAGATGGTTTAGAAACCAAAAATAAGCACCACACAAAAGCAGATTATACATACACCATCAGGCCTTTGGAATATTAAGGCAACATAAATATCTCAAGCAATTTTAGAAGAATGCTTTACTTATATAACAGATGTTATTAAAACATCTCAAAAGAGGCAGGGCTCACAATTTTTTTCAGTATGAGGTCTTCCCTTCCATTTTTGTTAATATATTAATGATTCTTCTTAAATACTGTACCATAATTAGTCTAGATTAACAAATGGGCTATCAAAGCCACTATCTTGTTGGCTAGATAGCGGAACAATTAATTTTCTTGAAGGCTGCTGACACACTGAAGATGGTAATGTACTGCTCAGTTTTTTGAAATCTGACTTTAATCTATCAGCCTTATGACGAGATGGGTGTCCACAATTCACACTGATCTTTCCTGGCTCCAAATACGTGGTTTCTTCTGACAGGTATGGAGTTTGATAACGCTGACATTTCATTGTTTGACAAATCATATTACTTTCCTCTGTATCTGAAAGATAACCGGATGGTGAAAACTGTTTGGATTTAACAGATTCACTTGGTATTTCCAAAGTTCCTTGTGGCCTACCATGTACAAATGATGCTTCACGACTGTCAAAGGATAAGGTTGCACTGCTGGAAGGCCAGCCCAAGCAGTCACTAAGGTCC-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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]

ACMG classification

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

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Mar 16, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-49030150;