dbSNP rs17636091: PRC1:c.1351-3C>T (chr15-90974249-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003981.4(PRC1):c.1351-3C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 1,609,786 control chromosomes in the GnomAD database, including 13,909 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.10 ( 1465 hom., cov: 32)

Exomes 𝑓: 0.099 ( 12444 hom. )

Consequence

PRC1
NM_003981.4 splice_region, intron

Scores

Splicing: ADA: 0.0002213

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 1.60

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:

ENSG00000284946 (HGNC:):

ENSG00000284946 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRC1	NM_003981.4 link	c.1351-3C>T		splice_region_variant, intron_variant	Intron 10 of 14	ENST00000394249.8	NP_003972.2	O43663-1A0A024RC67

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRC1	ENST00000394249.8 link	c.1351-3C>T		splice_region_variant, intron_variant	Intron 10 of 14	1	NM_003981.4	ENSP00000377793.3		O43663-1
ENSG00000284946	ENST00000643536.1 link	n.*1314-3C>T		splice_region_variant, intron_variant	Intron 31 of 34			ENSP00000494429.1		A0A2R8YDQ0

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15671

AN:

152176

Hom.:

1464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.0798

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.0729

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0760

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.151

AC:

38012

AN:

251280

Hom.:

5014

AF XY:

0.146

AC XY:

19813

AN XY:

135810

show subpopulations

Gnomad AFR exome

AF:

0.0479

Gnomad AMR exome

AF:

0.319

Gnomad ASJ exome

AF:

0.0723

Gnomad EAS exome

AF:

0.470

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.0743

Gnomad NFE exome

AF:

0.0746

Gnomad OTH exome

AF:

0.133

GnomAD4 exome

AF:

0.0995

AC:

145004

AN:

1457492

Hom.:

12444

Cov.:

AF XY:

0.101

AC XY:

73366

AN XY:

725356

show subpopulations

Gnomad4 AFR exome

AF:

0.0454

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.0727

Gnomad4 EAS exome

AF:

0.488

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.0757

Gnomad4 NFE exome

AF:

0.0728

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.103

AC:

15671

AN:

152294

Hom.:

1465

Cov.:

AF XY:

0.109

AC XY:

8139

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0492

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.0798

Gnomad4 EAS

AF:

0.465

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.0729

Gnomad4 NFE

AF:

0.0760

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.0966

Hom.:

607

Bravo

AF:

0.115

Asia WGS

AF:

0.293

AC:

1017

AN:

3478

EpiCase

AF:

0.0838

EpiControl

AF:

0.0896

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Familial cancer of breast

Uncertain:1

Feb 01, 2014

Research Lab, National Institute of Public Health

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

4.7

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00022

dbscSNV1_RF

Benign

0.076

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