Variant chr15-90966362-T-C 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.*769A>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 0.432 in 319,920 control chromosomes in the GnomAD database, including 36,268 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 0.47 ( 20288 hom., cov: 32)

Exomes 𝑓: 0.40 ( 15980 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:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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.*769A>G		3_prime_UTR_variant	15/15	ENST00000394249.8	NP_003972.2
PRC1-AS1	NR_051984.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRC1	ENST00000394249.8 linkuse as main transcript	c.*769A>G		3_prime_UTR_variant	15/15	1	NM_003981.4	ENSP00000377793		O43663-1
PRC1-AS1	ENST00000554388.2 linkuse as main transcript	n.23T>C		non_coding_transcript_exon_variant	1/4	2

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71632

AN:

151886

Hom.:

20238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.590

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.988

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.486

GnomAD4 exome

AF:

0.397

AC:

66604

AN:

167916

Hom.:

15980

Cov.:

AF XY:

0.409

AC XY:

37934

AN XY:

92754

show subpopulations

Gnomad4 AFR exome

AF:

0.712

Gnomad4 AMR exome

AF:

0.646

Gnomad4 ASJ exome

AF:

0.343

Gnomad4 EAS exome

AF:

0.995

Gnomad4 SAS exome

AF:

0.495

Gnomad4 FIN exome

AF:

0.302

Gnomad4 NFE exome

AF:

0.288

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.472

AC:

71749

AN:

152004

Hom.:

20288

Cov.:

AF XY:

0.479

AC XY:

35616

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.988

Gnomad4 SAS

AF:

0.523

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.491

Alfa

AF:

0.348

Hom.:

15530

Bravo

AF:

0.508

Asia WGS

AF:

0.749

AC:

2600

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.7

DANN

Benign

0.59

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