rs8042680

Variant names:

• chr15-90978107-C-A
• rs8042680
• NM_003981.4:c.1107+1051G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-90978107-C-A
• chr15-90978107-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003981.4(PRC1):​c.1107+1051G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,136 control chromosomes in the GnomAD database, including 27,206 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (27206 hom., cov: 31)
• Consequence: PRC1 NM_003981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 152 publications found

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]

ENSG00000284946 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003981.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRC1	NM_003981.4	MANE Select	c.1107+1051G>T		intron	N/A	NP_003972.2	O43663-1
	PRC1	NM_199413.3		c.1107+1051G>T		intron	N/A	NP_955445.2	O43663-4
	PRC1	NM_001267580.2		c.984+1051G>T		intron	N/A	NP_001254509.2	O43663-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRC1	ENST00000394249.8	TSL:1 MANE Select	c.1107+1051G>T		intron	N/A	ENSP00000377793.3	O43663-1
	PRC1	ENST00000361188.9	TSL:1	c.1107+1051G>T		intron	N/A	ENSP00000354679.5	O43663-4
	ENSG00000284946	ENST00000643536.1		n.*1070+1051G>T		intron	N/A	ENSP00000494429.1	A0A2R8YDQ0

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82147 AN: 152018 Hom.: 27137 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.541 AC: 82282 AN: 152136 Hom.: 27206 Cov.: 31 AF XY: 0.548 AC XY: 40738 AN XY: 74364

African (AFR) AF: 0.866 AC: 35973 AN: 41526

American (AMR) AF: 0.621 AC: 9480 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5133 AN: 5178

South Asian (SAS) AF: 0.657 AC: 3167 AN: 4822

European-Finnish (FIN) AF: 0.330 AC: 3489 AN: 10578

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21929 AN: 67980

Other (OTH) AF: 0.550 AC: 1159 AN: 2108

Alfa AF: 0.397 Hom.: 64162

Bravo AF: 0.580

Asia WGS AF: 0.845 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.31
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8042680; hg19: chr15-91521337;