rs4669700

Positions:

• chr2-11261412-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004850.5(ROCK2):​c.325-11614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,192 control chromosomes in the GnomAD database, including 3,742 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 0.20 (3742 hom., cov: 33)
• Consequence: ROCK2 NM_004850.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

ROCK2 (HGNC:10252): (Rho associated coiled-coil containing protein kinase 2) The protein encoded by this gene is a serine/threonine kinase that regulates cytokinesis, smooth muscle contraction, the formation of actin stress fibers and focal adhesions, and the activation of the c-fos serum response element. This protein, which is an isozyme of ROCK1 is a target for the small GTPase Rho. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ROCK2	NM_004850.5	c.325-11614A>G		intron_variant		ENST00000315872.11	NP_004841.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ROCK2	ENST00000315872.11	c.325-11614A>G		intron_variant		1	NM_004850.5	ENSP00000317985	P2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30813 AN: 152074 Hom.: 3744 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.203 AC: 30822 AN: 152192 Hom.: 3742 Cov.: 33 AF XY: 0.209 AC XY: 15529 AN XY: 74402

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.244

Alfa AF: 0.216 Hom.: 4949

Bravo AF: 0.199

Asia WGS AF: 0.425 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669700; hg19: chr2-11401538;