rs15172

Variant names:

• chr15-90966212-C-A
• rs15172
• NM_003981.4:c.*919G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-90966212-C-A
• chr15-90966212-C-T

Variant summary

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

The NM_003981.4(PRC1):​c.*919G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 196,124 control chromosomes in the GnomAD database, including 611 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 0.050 (592 hom., cov: 32)
  • Exomes 𝑓: 0.0084 (19 hom.)
• Consequence: PRC1 NM_003981.4 3_prime_UTR
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.561
• Publications: 4 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 (REVEL=0.006).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 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.*919G>T		3_prime_UTR	Exon 15 of 15	NP_003972.2	O43663-1
	PRC1	NM_199413.3		c.*919G>T		3_prime_UTR	Exon 14 of 14	NP_955445.2	O43663-4
	PRC1	NM_001267580.2		c.*962G>T		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.*919G>T		3_prime_UTR	Exon 15 of 15	ENSP00000377793.3	O43663-1
	PRC1	ENST00000361188.9	TSL:1	c.*919G>T		3_prime_UTR	Exon 14 of 14	ENSP00000354679.5	O43663-4
	ENSG00000284946	ENST00000643536.1		n.*4544G>T		non_coding_transcript_exon	Exon 35 of 35	ENSP00000494429.1	A0A2R8YDQ0

Frequencies

GnomAD3 genomes AF: 0.0501 AC: 7620 AN: 152084 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00203

Gnomad OTH AF: 0.0440

GnomAD4 exome AF: 0.00840 AC: 369 AN: 43922 Hom.: 19 Cov.: 0 AF XY: 0.00782 AC XY: 180 AN XY: 23004

African (AFR) AF: 0.149 AC: 209 AN: 1404

American (AMR) AF: 0.0128 AC: 34 AN: 2646

Ashkenazi Jewish (ASJ) AF: 0.0270 AC: 28 AN: 1036

East Asian (EAS) AF: 0.00135 AC: 3 AN: 2228

South Asian (SAS) AF: 0.00459 AC: 28 AN: 6102

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2324

Middle Eastern (MID) AF: 0.0294 AC: 6 AN: 204

European-Non Finnish (NFE) AF: 0.00145 AC: 37 AN: 25446

Other (OTH) AF: 0.00948 AC: 24 AN: 2532

GnomAD4 genome AF: 0.0502 AC: 7646 AN: 152202 Hom.: 592 Cov.: 32 AF XY: 0.0481 AC XY: 3575 AN XY: 74390

African (AFR) AF: 0.167 AC: 6944 AN: 41510

American (AMR) AF: 0.0213 AC: 326 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.00601 AC: 29 AN: 4822

European-Finnish (FIN) AF: 0.0000944 AC: 1 AN: 10588

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00201 AC: 137 AN: 68020

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0279 Hom.: 157

Bravo AF: 0.0575

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Familial cancer of breast (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.79
PhyloP100		-0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs15172; hg19: chr15-91509442;