15-90966398-C-G

Variant names:

• chr15-90966398-C-G
• rs112770009
• NM_003981.4:c.*733G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003981.4(PRC1):​c.*733G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000532 in 188,056 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000053 (0 hom.)
• Consequence: PRC1 NM_003981.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.015).

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.*733G>C		3_prime_UTR	Exon 15 of 15	NP_003972.2	O43663-1
	PRC1	NM_199413.3		c.*733G>C		3_prime_UTR	Exon 14 of 14	NP_955445.2	O43663-4
	PRC1	NM_001267580.2		c.*776G>C		3_prime_UTR	Exon 13 of 13	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.*733G>C		3_prime_UTR	Exon 15 of 15	ENSP00000377793.3	O43663-1
	PRC1	ENST00000361188.9	TSL:1	c.*733G>C		3_prime_UTR	Exon 14 of 14	ENSP00000354679.5	O43663-4
	ENSG00000284946	ENST00000643536.1		n.*4358G>C		non_coding_transcript_exon	Exon 35 of 35	ENSP00000494429.1	A0A2R8YDQ0

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000532 AC: 1 AN: 188056 Hom.: 0 Cov.: 0 AF XY: 0.00000955 AC XY: 1 AN XY: 104734

African (AFR) AF: 0.00 AC: 0 AN: 4772

American (AMR) AF: 0.00 AC: 0 AN: 11992

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4424

East Asian (EAS) AF: 0.00 AC: 0 AN: 7030

South Asian (SAS) AF: 0.00 AC: 0 AN: 40760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8758

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 668

European-Non Finnish (NFE) AF: 0.00000992 AC: 1 AN: 100758

Other (OTH) AF: 0.00 AC: 0 AN: 8894

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.57
PhyloP100		0.34

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: rs112770009; hg19: chr15-91509628;