13-24882779-T-C

Position:

• chr13-24882779-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018451.5(CENPJ):​c.*398A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 197,026 control chromosomes in the GnomAD database, including 1,769 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1346 hom., cov: 31)
  • Exomes 𝑓: 0.12 (423 hom.)
• Consequence: CENPJ NM_018451.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.627

Genes affected

CENPJ (HGNC:17272): (centromere protein J) This gene encodes a protein that belongs to the centromere protein family. During cell division, this protein plays a structural role in the maintenance of centrosome integrity and normal spindle morphology, and it is involved in microtubule disassembly at the centrosome. This protein can function as a transcriptional coactivator in the Stat5 signaling pathway, and also as a coactivator of NF-kappaB-mediated transcription, likely via its interaction with the coactivator p300/CREB-binding protein. Mutations in this gene are associated with primary autosomal recessive microcephaly, a disorder characterized by severely reduced brain size and cognitive disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2012]

RNF17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 13-24882779-T-C is Benign according to our data. Variant chr13-24882779-T-C is described in ClinVar as [Benign]. Clinvar id is 311598.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CENPJ	NM_018451.5	c.*398A>G		3_prime_UTR_variant	17/17	ENST00000381884.9	NP_060921.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CENPJ	ENST00000381884.9	c.*398A>G		3_prime_UTR_variant	17/17	1	NM_018451.5	ENSP00000371308	P1
CENPJ	ENST00000616936.4	c.*1069A>G		3_prime_UTR_variant, NMD_transcript_variant	16/16	1		ENSP00000477511

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17735 AN: 152048 Hom.: 1344 Cov.: 31

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.0924

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.121 AC: 5412 AN: 44860 Hom.: 423 Cov.: 0 AF XY: 0.115 AC XY: 2700 AN XY: 23460

Gnomad4 AFR exome AF: 0.0215

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.0432

Gnomad4 EAS exome AF: 0.268

Gnomad4 SAS exome AF: 0.0713

Gnomad4 FIN exome AF: 0.175

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.145

GnomAD4 genome AF: 0.117 AC: 17738 AN: 152166 Hom.: 1346 Cov.: 31 AF XY: 0.118 AC XY: 8795 AN XY: 74380

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.0931

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.120

Alfa AF: 0.124 Hom.: 159

Bravo AF: 0.114

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Seckel syndrome 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Microcephaly 6, primary, autosomal recessive Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11620289; hg19: chr13-25456917;