18-139767-C-T

Variant names:

• chr18-139767-C-T
• rs4797697
• ENST00000755797.1:n.398-1714C>T

Variant summary

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

The ENST00000755797.1(ROCK1P1):​n.398-1714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,724 control chromosomes in the GnomAD database, including 7,746 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 0.32 (7746 hom., cov: 31)
• Consequence: ROCK1P1 ENST00000755797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 6 publications found

Genes affected

ROCK1P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755797.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROCK1P1	ENST00000755797.1		n.398-1714C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48127 AN: 151606 Hom.: 7722 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.318 AC: 48201 AN: 151724 Hom.: 7746 Cov.: 31 AF XY: 0.316 AC XY: 23458 AN XY: 74122

African (AFR) AF: 0.321 AC: 13263 AN: 41360

American (AMR) AF: 0.368 AC: 5604 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5154

South Asian (SAS) AF: 0.297 AC: 1420 AN: 4780

European-Finnish (FIN) AF: 0.317 AC: 3325 AN: 10496

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21313 AN: 67920

Other (OTH) AF: 0.325 AC: 684 AN: 2102

Alfa AF: 0.317 Hom.: 30072

Bravo AF: 0.328

Asia WGS AF: 0.303 AC: 1056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4797697; hg19: chr18-139767;