17-7944637-C-G

Position:

• chr17-7944637-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_053051.5(CNTROB):​c.1733C>G​(p.Pro578Arg) variant causes a missense, splice region 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. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P578Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CNTROB NM_053051.5 missense, splice_region
• Scores: Splicing: ADA: 0.0001549
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

CNTROB (HGNC:29616): (centrobin, centriole duplication and spindle assembly protein) This gene encodes a centrosomal protein that interacts with BRCA2, and is required for centriole duplication and cytokinesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06582159).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTROB	NM_053051.5	c.1733C>G	p.Pro578Arg	missense_variant, splice_region_variant	12/19	ENST00000563694.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTROB	ENST00000563694.6	c.1733C>G	p.Pro578Arg	missense_variant, splice_region_variant	12/19	1	NM_053051.5	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 49

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	6.9
DANN	Benign	0.94
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.67	T;T;T
M_CAP	Benign	0.0089	T
MetaRNN	Benign	0.066	T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Uncertain	2.3	M;M;M
MutationTaster	Benign	1.0	P;P;P;P
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.46	N;N;N
REVEL	Benign	0.021
Sift	Benign	0.22	T;T;T
Sift4G	Benign	0.10	T;T;T
Polyphen		0.16	B;B;B
Vest4		0.11
MutPred		0.16		Loss of glycosylation at P578 (P = 0.0029);Loss of glycosylation at P578 (P = 0.0029);Loss of glycosylation at P578 (P = 0.0029);
MVP		0.27
MPC		0.33
ClinPred		0.056	T
GERP RS		-2.4
Varity_R		0.022
gMVP		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00015
dbscSNV1_RF	Benign	0.10
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: rs11650083; hg19: chr17-7847955;