chr2-11207815-T-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_004850.5(ROCK2):āc.2460A>Cā(p.Leu820=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,612,994 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0070 ( 14 hom., cov: 33)
Exomes š: 0.00069 ( 10 hom. )
Consequence
ROCK2
NM_004850.5 synonymous
NM_004850.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.218
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 2-11207815-T-G is Benign according to our data. Variant chr2-11207815-T-G is described in ClinVar as [Benign]. Clinvar id is 3052771.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.218 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00698 (1063/152338) while in subpopulation AFR AF= 0.0243 (1011/41582). AF 95% confidence interval is 0.0231. There are 14 homozygotes in gnomad4. There are 521 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1063 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROCK2 | NM_004850.5 | c.2460A>C | p.Leu820= | synonymous_variant | 20/33 | ENST00000315872.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROCK2 | ENST00000315872.11 | c.2460A>C | p.Leu820= | synonymous_variant | 20/33 | 1 | NM_004850.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00701 AC: 1067AN: 152220Hom.: 14 Cov.: 33
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GnomAD3 exomes AF: 0.00156 AC: 388AN: 249176Hom.: 3 AF XY: 0.00107 AC XY: 145AN XY: 135192
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GnomAD4 exome AF: 0.000691 AC: 1009AN: 1460656Hom.: 10 Cov.: 30 AF XY: 0.000572 AC XY: 416AN XY: 726686
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GnomAD4 genome ? AF: 0.00698 AC: 1063AN: 152338Hom.: 14 Cov.: 33 AF XY: 0.00699 AC XY: 521AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ROCK2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at