NM_144600.4:c.479G>A

Variant names:

• chr16-15867486-C-T
• NM_144600.4:c.479G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144600.4(CEP20):​c.479G>A​(p.Ser160Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CEP20 NM_144600.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.380
• Publications: 0 publications found

Genes affected

CEP20 (HGNC:26435): (centrosomal protein 20) Enables identical protein binding activity. Involved in cilium assembly. Located in centriolar satellite and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.047214538).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144600.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP20	NM_144600.4	MANE Select	c.479G>A	p.Ser160Asn	missense	Exon 5 of 5	NP_653201.1	Q96NB1-1
	CEP20	NM_001304499.2		c.551G>A	p.Ser184Asn	missense	Exon 6 of 6	NP_001291428.1	I3NI25
	CEP20	NM_001304500.2		c.281G>A	p.Ser94Asn	missense	Exon 4 of 4	NP_001291429.1	I3L269

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP20	ENST00000255759.11	TSL:1 MANE Select	c.479G>A	p.Ser160Asn	missense	Exon 5 of 5	ENSP00000255759.6	Q96NB1-1
	CEP20	ENST00000929533.1		c.659G>A	p.Ser220Asn	missense	Exon 7 of 7	ENSP00000599592.1
	CEP20	ENST00000962008.1		c.632G>A	p.Ser211Asn	missense	Exon 6 of 6	ENSP00000632067.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.8
DANN	Benign	0.83
DEOGEN2	Benign	0.0082	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.063	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.0056	T
MetaRNN	Benign	0.047	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	L
PhyloP100		0.38
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-0.27	N
REVEL	Benign	0.011
Sift	Benign	0.56	T
Sift4G	Benign	0.34	T
Polyphen		0.0	B
Vest4		0.017
MutPred		0.11		Loss of phosphorylation at S160 (P = 0.0419)
MVP		0.030
MPC		0.015
ClinPred		0.026	T
GERP RS		-1.5
Varity_R		0.016
gMVP		0.073

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

hg19: chr16-15961343;