rs570505

Variant names:

• chr18-13047785-T-G
• rs570505
• NM_032142.4:c.2068-1074T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CEP192	NM_032142.4	c.2068-1074T>G		intron_variant	Intron 15 of 44	ENST00000506447.5	NP_115518.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP192	ENST00000506447.5	c.2068-1074T>G		intron_variant	Intron 15 of 44	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

African (AFR) AF: 0.889 AC: 36885 AN: 41470

American (AMR) AF: 0.676 AC: 10313 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2531 AN: 3466

East Asian (EAS) AF: 0.805 AC: 4166 AN: 5174

South Asian (SAS) AF: 0.704 AC: 3394 AN: 4818

European-Finnish (FIN) AF: 0.610 AC: 6427 AN: 10538

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41660 AN: 67956

Other (OTH) AF: 0.717 AC: 1515 AN: 2112

Alfa AF: 0.641 Hom.: 16208

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
PhyloP100		-0.88
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs570505; hg19: chr18-13047784;