Genetic Variant ROCK1P1:n.389+3082G>C (chr18-112535-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

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

The ENST00000608049.5(ROCK1P1):n.389+3082G>C variant causes a intron 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
ENST00000608049.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.194

Publications

7 publications found

Variant links:

Genes affected

ROCK1P1 (HGNC:):

ROCK1P1 links:

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

ROCK1P1 links:

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]

MIR8078 links:

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ACMG classification

Classification was made for transcript

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

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
ROCK1P1	NR_160777.1 link	n.438G>C	non_coding_transcript_exon_variant	Exon 1 of 5
ROCK1P1	NR_033770.1 link	n.389+3082G>C	intron_variant	Intron 1 of 4
ROCK1P1	NR_160778.1 link	n.204+719G>C	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ROCK1P1	ENST00000608049.5 link	n.389+3082G>C	intron_variant	Intron 1 of 4	1
ROCK1P1	ENST00000576266.7 link	n.472G>C	non_coding_transcript_exon_variant	Exon 1 of 5	4
ROCK1P1	ENST00000755797.1 link	n.91G>C	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

103472

Hom.:

Cov.:

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:

AN:

382512

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

210648

African (AFR)

AF:

0.00

AC:

AN:

7466

American (AMR)

AF:

0.00

AC:

AN:

22798

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11484

East Asian (EAS)

AF:

0.00

AC:

AN:

27424

South Asian (SAS)

AF:

0.00

AC:

AN:

42390

European-Finnish (FIN)

AF:

0.00

AC:

AN:

34084

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1350

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

215554

Other (OTH)

AF:

0.00

AC:

AN:

19962

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

103558

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

50918

African (AFR)

AF:

0.00

AC:

AN:

24558

American (AMR)

AF:

0.00

AC:

AN:

11312

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2232

East Asian (EAS)

AF:

0.00

AC:

AN:

4328

South Asian (SAS)

AF:

0.00

AC:

AN:

3460

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8240

Middle Eastern (MID)

AF:

0.00

AC:

AN:

188

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

47210

Other (OTH)

AF:

0.00

AC:

AN:

1472

Alfa

AF:

0.0000556

Hom.:

8579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

0.19

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over