rs372967874

Variant names:

• chr15-48805535-CTTTTTTTTT-C
• NM_001194998.2:c.87+19_87+27delAAAAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr15-48805535-CTTTTTTTTT-C
• chr15-48805535-CTTTTTTTTT-CTT
• chr15-48805535-CTTTTTTTTT-CTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTTTTTT
• chr15-48805535-CTTTTTTTTT-CTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001194998.2(CEP152):​c.87+19_87+27delAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000266 in 1,128,246 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2	c.87+19_87+27delAAAAAAAAA		intron_variant	Intron 2 of 26	ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7	c.87+19_87+27delAAAAAAAAA		intron_variant	Intron 2 of 26	1	NM_001194998.2	ENSP00000370337.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000266 AC: 3 AN: 1128246 Hom.: 0 AF XY: 0.00000177 AC XY: 1 AN XY: 564898

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000346

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

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: chr15-49097732;