18-112535-G-C

Variant names:

• chr18-112535-G-C
• rs9284390
• ENST00000608049.5:n.389+3082G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000576266.7(ROCK1P1):​n.472G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ROCK1P1 ENST00000576266.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 7 publications found

Genes affected

ROCK1P1 (HGNC:):

ROCK1P1 (HGNC:37832): (Rho associated coiled-coil containing protein kinase 1 pseudogene 1)

MIR8078 (HGNC:50102): (microRNA 8078) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576266.7. 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
	ROCK1P1	NR_160777.1		n.438G>C		non_coding_transcript_exon	Exon 1 of 5
	ROCK1P1	NR_033770.1		n.389+3082G>C		intron	N/A
	ROCK1P1	NR_160778.1		n.204+719G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROCK1P1	ENST00000608049.5	TSL:1	n.389+3082G>C		intron	N/A
	ROCK1P1	ENST00000576266.7	TSL:4	n.472G>C		non_coding_transcript_exon	Exon 1 of 5
	ROCK1P1	ENST00000755797.1		n.91G>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 103472 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 382512 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 210648

African (AFR) AF: 0.00 AC: 0 AN: 7466

American (AMR) AF: 0.00 AC: 0 AN: 22798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11484

East Asian (EAS) AF: 0.00 AC: 0 AN: 27424

South Asian (SAS) AF: 0.00 AC: 0 AN: 42390

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34084

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1350

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 215554

Other (OTH) AF: 0.00 AC: 0 AN: 19962

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 103558 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 50918

African (AFR) AF: 0.00 AC: 0 AN: 24558

American (AMR) AF: 0.00 AC: 0 AN: 11312

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2232

East Asian (EAS) AF: 0.00 AC: 0 AN: 4328

South Asian (SAS) AF: 0.00 AC: 0 AN: 3460

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 188

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 47210

Other (OTH) AF: 0.00 AC: 0 AN: 1472

Alfa AF: 0.0000556 Hom.: 8579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	10
DANN	Benign	0.62
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9284390; hg19: chr18-112535;