rs921322

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004850.5(ROCK2):​c.*3903C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,940 control chromosomes in the GnomAD database, including 13,412 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 0.40 ( 13412 hom., cov: 32)

Consequence

ROCK2
NM_004850.5 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ROCK2NM_004850.5 linkc.*3903C>T downstream_gene_variant ENST00000315872.11 NP_004841.2 O75116A0A2P9DU05Q14DU5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ROCK2ENST00000315872.11 linkc.*3903C>T downstream_gene_variant 1 NM_004850.5 ENSP00000317985.6 O75116
ROCK2ENST00000697752.1 linkc.*3903C>T downstream_gene_variant ENSP00000513431.1 A0A8V8TL82
ROCK2ENST00000697790.1 linkc.*3920C>T downstream_gene_variant ENSP00000513442.1 A0A8V8TL90

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
60061
AN:
151822
Hom.:
13398
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.499
Gnomad AMR
AF:
0.514
Gnomad ASJ
AF:
0.413
Gnomad EAS
AF:
0.401
Gnomad SAS
AF:
0.506
Gnomad FIN
AF:
0.402
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.486
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.396
AC:
60095
AN:
151940
Hom.:
13412
Cov.:
32
AF XY:
0.395
AC XY:
29313
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.182
Gnomad4 AMR
AF:
0.515
Gnomad4 ASJ
AF:
0.413
Gnomad4 EAS
AF:
0.401
Gnomad4 SAS
AF:
0.506
Gnomad4 FIN
AF:
0.402
Gnomad4 NFE
AF:
0.486
Gnomad4 OTH
AF:
0.416
Alfa
AF:
0.480
Hom.:
23760
Bravo
AF:
0.392
Asia WGS
AF:
0.424
AC:
1477
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.4
DANN
Benign
0.55

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs921322; hg19: chr2-11319660; API