Variant 15-90966690-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_003981.4(PRC1):c.*441C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 455,830 control chromosomes in the GnomAD database, including 1,451 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 0.058 ( 311 hom., cov: 32)

Exomes 𝑓: 0.076 ( 1140 hom. )

Consequence

PRC1
NM_003981.4 3_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.844

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRC1	NM_003981.4 linkuse as main transcript	c.*441C>A		3_prime_UTR_variant	15/15	ENST00000394249.8	NP_003972.2
PRC1-AS1	NR_051984.1 linkuse as main transcript	n.310+12G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRC1	ENST00000394249.8 linkuse as main transcript	c.*441C>A		3_prime_UTR_variant	15/15	1	NM_003981.4	ENSP00000377793		O43663-1
PRC1-AS1	ENST00000554388.2 linkuse as main transcript	n.339+12G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0583

AC:

8868

AN:

152148

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0351

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0403

Gnomad ASJ

AF:

0.0767

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0727

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0711

Gnomad OTH

AF:

0.0584

GnomAD3 exomes

AF:

0.0671

AC:

8676

AN:

129376

Hom.:

466

AF XY:

0.0730

AC XY:

5157

AN XY:

70628

show subpopulations

Gnomad AFR exome

AF:

0.0312

Gnomad AMR exome

AF:

0.0276

Gnomad ASJ exome

AF:

0.0757

Gnomad EAS exome

AF:

0.00202

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.0657

Gnomad NFE exome

AF:

0.0705

Gnomad OTH exome

AF:

0.0606

GnomAD4 exome

AF:

0.0756

AC:

22947

AN:

303564

Hom.:

1140

Cov.:

AF XY:

0.0821

AC XY:

14186

AN XY:

172850

show subpopulations

Gnomad4 AFR exome

AF:

0.0338

Gnomad4 AMR exome

AF:

0.0277

Gnomad4 ASJ exome

AF:

0.0752

Gnomad4 EAS exome

AF:

0.00206

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.0637

Gnomad4 NFE exome

AF:

0.0695

Gnomad4 OTH exome

AF:

0.0686

GnomAD4 genome

AF:

0.0582

AC:

8865

AN:

152266

Hom.:

311

Cov.:

AF XY:

0.0581

AC XY:

4328

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0351

Gnomad4 AMR

AF:

0.0403

Gnomad4 ASJ

AF:

0.0767

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.0727

Gnomad4 NFE

AF:

0.0710

Gnomad4 OTH

AF:

0.0578

Alfa

AF:

0.0509

Hom.:

Bravo

AF:

0.0527

Asia WGS

AF:

0.0910

AC:

317

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

-0.38

CADD

Benign

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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