rs570505

Positions:

• chr18-13047785-T-G

Variant summary

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

The NM_032142.4(CEP192):​c.2068-1074T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,002 control chromosomes in the GnomAD database, including 39,336 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 0.71 (39336 hom., cov: 32)
• Consequence: CEP192 NM_032142.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

Genes affected

CEP192 (HGNC:25515): (centrosomal protein 192) Enables phosphatase binding activity. Involved in centrosome-templated microtubule nucleation; mitotic spindle assembly; and protein localization to centrosome. Located in centriole; centrosome; and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP192	NM_032142.4	c.2068-1074T>G		intron_variant		ENST00000506447.5	NP_115518.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP192	ENST00000506447.5	c.2068-1074T>G		intron_variant		5	NM_032142.4	ENSP00000427550.1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107595 AN: 151884 Hom.: 39282 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.709 AC: 107704 AN: 152002 Hom.: 39336 Cov.: 32 AF XY: 0.709 AC XY: 52665 AN XY: 74276

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.717

Alfa AF: 0.640 Hom.: 14363

Bravo AF: 0.722

Asia WGS AF: 0.808 AC: 2802 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs570505; hg19: chr18-13047784;