NM_001194998.2:c.2695-1073G>A

Variant names:

• chr15-48757626-C-T
• rs1968825
• NM_001194998.2:c.2695-1073G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001194998.2(CEP152):​c.2695-1073G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,236 control chromosomes in the GnomAD database, including 64,662 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64662 hom., cov: 31)
• Consequence: CEP152 NM_001194998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.52

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP152	NM_001194998.2	c.2695-1073G>A		intron_variant	Intron 19 of 26	ENST00000380950.7	NP_001181927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP152	ENST00000380950.7	c.2695-1073G>A		intron_variant	Intron 19 of 26	1	NM_001194998.2	ENSP00000370337.2
CEP152	ENST00000399334.7	c.2695-1073G>A		intron_variant	Intron 19 of 25	1		ENSP00000382271.3
CEP152	ENST00000325747.9	c.2416-1073G>A		intron_variant	Intron 18 of 24	1		ENSP00000321000.5

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139941 AN: 152118 Hom.: 64613 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.920 AC: 140041 AN: 152236 Hom.: 64662 Cov.: 31 AF XY: 0.917 AC XY: 68240 AN XY: 74430

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.913

Alfa AF: 0.956 Hom.: 3836

Bravo AF: 0.907

Asia WGS AF: 0.811 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0020
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1968825; hg19: chr15-49049823;