rs2290203

Variant names:

• chr15-90968837-G-A
• rs2290203
• NM_003981.4:c.1791+242C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-90968837-G-A
• chr15-90968837-G-C
• chr15-90968837-G-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.1791+242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 1,314,436 control chromosomes in the GnomAD database, including 37,985 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 0.29 (7172 hom., cov: 32)
  • Exomes 𝑓: 0.22 (30813 hom.)
• Consequence: PRC1 NM_003981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 50 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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.1791+242C>T		intron	N/A	NP_003972.2	O43663-1
	PRC1	NM_199413.3		c.1749+610C>T		intron	N/A	NP_955445.2	O43663-4
	PRC1	NM_001267580.2		c.1549+687C>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.1791+242C>T		intron	N/A	ENSP00000377793.3	O43663-1
	PRC1	ENST00000361188.9	TSL:1	c.1749+610C>T		intron	N/A	ENSP00000354679.5	O43663-4
	ENSG00000284946	ENST00000643536.1		n.*1919C>T		non_coding_transcript_exon	Exon 35 of 35	ENSP00000494429.1	A0A2R8YDQ0

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44001 AN: 151968 Hom.: 7147 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.220 AC: 255818 AN: 1162350 Hom.: 30813 Cov.: 31 AF XY: 0.222 AC XY: 123931 AN XY: 558882

African (AFR) AF: 0.420 AC: 10696 AN: 25496

American (AMR) AF: 0.326 AC: 5324 AN: 16318

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 3105 AN: 14962

East Asian (EAS) AF: 0.488 AC: 12788 AN: 26218

South Asian (SAS) AF: 0.339 AC: 18076 AN: 53324

European-Finnish (FIN) AF: 0.217 AC: 4616 AN: 21228

Middle Eastern (MID) AF: 0.232 AC: 698 AN: 3012

European-Non Finnish (NFE) AF: 0.198 AC: 189221 AN: 955900

Other (OTH) AF: 0.246 AC: 11294 AN: 45892

GnomAD4 genome AF: 0.290 AC: 44065 AN: 152086 Hom.: 7172 Cov.: 32 AF XY: 0.292 AC XY: 21728 AN XY: 74360

African (AFR) AF: 0.408 AC: 16925 AN: 41480

American (AMR) AF: 0.309 AC: 4730 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2580 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2471 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14037 AN: 67974

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.231 Hom.: 12446

Bravo AF: 0.302

Asia WGS AF: 0.466 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		0.042
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: rs2290203; hg19: chr15-91512067;