rs9284390

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-112535-G-A
• chr18-112535-G-C
• chr18-112535-G-T

Variant summary

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

The ENST00000608049.5(ROCK1P1):​n.389+3082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 476,220 control chromosomes in the GnomAD database, including 31,811 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 0.38 (5212 hom., cov: 30)
  • Exomes 𝑓: 0.44 (26599 hom.)
• Consequence: ROCK1P1 ENST00000608049.5 intron
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROCK1P1	NR_160777.1	n.438G>A		non_coding_transcript_exon_variant	Exon 1 of 5
ROCK1P1	NR_033770.1	n.389+3082G>A		intron_variant	Intron 1 of 4
ROCK1P1	NR_160778.1	n.204+719G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROCK1P1	ENST00000608049.5	n.389+3082G>A		intron_variant	Intron 1 of 4	1
ROCK1P1	ENST00000576266.7	n.472G>A		non_coding_transcript_exon_variant	Exon 1 of 5	4
ROCK1P1	ENST00000755797.1	n.91G>A		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.381 AC: 38655 AN: 101396 Hom.: 5202 Cov.: 30

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.286

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.440 AC: 165060 AN: 374740 Hom.: 26599 Cov.: 0 AF XY: 0.437 AC XY: 90221 AN XY: 206582

African (AFR) AF: 0.265 AC: 1911 AN: 7202

American (AMR) AF: 0.535 AC: 12021 AN: 22450

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 4144 AN: 11202

East Asian (EAS) AF: 0.636 AC: 17252 AN: 27110

South Asian (SAS) AF: 0.465 AC: 19488 AN: 41910

European-Finnish (FIN) AF: 0.462 AC: 15506 AN: 33550

Middle Eastern (MID) AF: 0.343 AC: 448 AN: 1308

European-Non Finnish (NFE) AF: 0.409 AC: 86067 AN: 210504

Other (OTH) AF: 0.422 AC: 8223 AN: 19504

GnomAD4 genome AF: 0.381 AC: 38692 AN: 101480 Hom.: 5212 Cov.: 30 AF XY: 0.389 AC XY: 19362 AN XY: 49830

African (AFR) AF: 0.251 AC: 5981 AN: 23868

American (AMR) AF: 0.452 AC: 5022 AN: 11104

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 776 AN: 2168

East Asian (EAS) AF: 0.579 AC: 2482 AN: 4284

South Asian (SAS) AF: 0.427 AC: 1445 AN: 3382

European-Finnish (FIN) AF: 0.471 AC: 3818 AN: 8112

Middle Eastern (MID) AF: 0.280 AC: 52 AN: 186

European-Non Finnish (NFE) AF: 0.396 AC: 18381 AN: 46404

Other (OTH) AF: 0.394 AC: 566 AN: 1436

Alfa AF: 0.274 Hom.: 8579

Asia WGS AF: 0.427 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.83
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;