Variant chr15-90966504-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003981.4(PRC1):c.*627T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 451,644 control chromosomes in the GnomAD database, including 1,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.080 ( 539 hom., cov: 32)

Exomes 𝑓: 0.085 ( 1266 hom. )

Consequence

PRC1
NM_003981.4 3_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.355

Variant links:

Genes affected

PRC1 (HGNC:9341): (protein regulator of cytokinesis 1) This gene encodes a protein that is involved in cytokinesis. The protein is present at high levels during the S and G2/M phases of mitosis but its levels drop dramatically when the cell exits mitosis and enters the G1 phase. It is located in the nucleus during interphase, becomes associated with mitotic spindles in a highly dynamic manner during mitosis, and localizes to the cell mid-body during cytokinesis. This protein has been shown to be a substrate of several cyclin-dependent kinases (CDKs). It is necessary for polarizing parallel microtubules and concentrating the factors responsible for contractile ring assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

PRC1 links:

PRC1-AS1 (HGNC:48587): (PRC1 antisense RNA 1)

PRC1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRC1	NM_003981.4 linkuse as main transcript	c.*627T>C		3_prime_UTR_variant	15/15	ENST00000394249.8
PRC1-AS1	NR_051984.1 linkuse as main transcript	n.136A>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRC1	ENST00000394249.8 linkuse as main transcript	c.*627T>C		3_prime_UTR_variant	15/15	1	NM_003981.4		O43663-1
PRC1-AS1	ENST00000554388.2 linkuse as main transcript	n.165A>G		non_coding_transcript_exon_variant	1/4	2

Frequencies

GnomAD3 genomes

AF:

0.0803

AC:

12219

AN:

152154

Hom.:

541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0808

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.0646

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.0209

Gnomad SAS

AF:

0.0990

Gnomad FIN

AF:

0.0580

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0855

Gnomad OTH

AF:

0.0923

GnomAD4 exome

AF:

0.0849

AC:

25414

AN:

299372

Hom.:

1266

Cov.:

AF XY:

0.0873

AC XY:

14868

AN XY:

170352

show subpopulations

Gnomad4 AFR exome

AF:

0.0789

Gnomad4 AMR exome

AF:

0.0476

Gnomad4 ASJ exome

AF:

0.135

Gnomad4 EAS exome

AF:

0.0208

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0720

Gnomad4 NFE exome

AF:

0.0850

Gnomad4 OTH exome

AF:

0.0888

GnomAD4 genome

AF:

0.0803

AC:

12231

AN:

152272

Hom.:

539

Cov.:

AF XY:

0.0800

AC XY:

5956

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0807

Gnomad4 AMR

AF:

0.0645

Gnomad4 ASJ

AF:

0.131

Gnomad4 EAS

AF:

0.0210

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0580

Gnomad4 NFE

AF:

0.0855

Gnomad4 OTH

AF:

0.0914

Alfa

AF:

0.0787

Hom.:

116

Bravo

AF:

0.0790

Asia WGS

AF:

0.0540

AC:

187

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Familial cancer of breast

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Research Lab, National Institute of Public Health

Feb 01, 2014

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over