Variant chr15-90968030-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.1792-828T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 984,838 control chromosomes in the GnomAD database, including 94,196 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 0.57 ( 29280 hom., cov: 33)

Exomes 𝑓: 0.38 ( 64916 hom. )

Consequence

PRC1
NM_003981.4 intron

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -1.62

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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.1792-828T>C		intron_variant		ENST00000394249.8
PRC1-AS1	NR_051984.1 linkuse as main transcript	n.310+1352A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRC1	ENST00000394249.8 linkuse as main transcript	c.1792-828T>C		intron_variant		1	NM_003981.4		O43663-1
PRC1-AS1	ENST00000554388.2 linkuse as main transcript	n.339+1352A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

87014

AN:

152004

Hom.:

29211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.650

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.992

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.577

GnomAD4 exome

AF:

0.382

AC:

317769

AN:

832716

Hom.:

64916

Cov.:

AF XY:

0.381

AC XY:

146507

AN XY:

384568

show subpopulations

Gnomad4 AFR exome

AF:

0.918

Gnomad4 AMR exome

AF:

0.647

Gnomad4 ASJ exome

AF:

0.425

Gnomad4 EAS exome

AF:

0.994

Gnomad4 SAS exome

AF:

0.654

Gnomad4 FIN exome

AF:

0.391

Gnomad4 NFE exome

AF:

0.358

Gnomad4 OTH exome

AF:

0.455

GnomAD4 genome

AF:

0.573

AC:

87149

AN:

152122

Hom.:

29280

Cov.:

AF XY:

0.578

AC XY:

43002

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.651

Gnomad4 ASJ

AF:

0.442

Gnomad4 EAS

AF:

0.992

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.365

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.581

Alfa

AF:

0.436

Hom.:

6883

Bravo

AF:

0.611

Asia WGS

AF:

0.852

AC:

2959

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

-0.91

CADD

Benign

0.58

DANN

Benign

0.32

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.18

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