15-90971530-C-T

Position:

• chr15-90971530-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003981.4(PRC1):​c.1462-1016G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,794 control chromosomes in the GnomAD database, including 1,552 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.11 (1552 hom., cov: 31)
• Consequence: PRC1 NM_003981.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.281

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRC1	NM_003981.4	c.1462-1016G>A		intron_variant		ENST00000394249.8	NP_003972.2
PRC1-AS1	NR_051984.1	n.310+4852C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRC1	ENST00000394249.8	c.1462-1016G>A		intron_variant		1	NM_003981.4	ENSP00000377793
PRC1-AS1	ENST00000554388.2	n.339+4852C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16859 AN: 151684 Hom.: 1551 Cov.: 31

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.0826

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.124

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.111 AC: 16861 AN: 151794 Hom.: 1552 Cov.: 31 AF XY: 0.117 AC XY: 8691 AN XY: 74160

Gnomad4 AFR AF: 0.0780

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.0826

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.125

Alfa AF: 0.108 Hom.: 461

Bravo AF: 0.124

Asia WGS AF: 0.295 AC: 1023 AN: 3476

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Breast carcinoma Other:1

association, 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	-0.89
CADD	Benign	2.9
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs11852999; hg19: chr15-91514760;