chr3-49375563-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001664.4(RHOA):c.27G>A(p.Val9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,613,688 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0025 ( 5 hom., cov: 31)
Exomes 𝑓: 0.00026 ( 1 hom. )
Consequence
RHOA
NM_001664.4 synonymous
NM_001664.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.382
Genes affected
RHOA (HGNC:667): (ras homolog family member A) This gene encodes a member of the Rho family of small GTPases, which cycle between inactive GDP-bound and active GTP-bound states and function as molecular switches in signal transduction cascades. Rho proteins promote reorganization of the actin cytoskeleton and regulate cell shape, attachment, and motility. Overexpression of this gene is associated with tumor cell proliferation and metastasis. Multiple alternatively spliced variants have been identified. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 3-49375563-C-T is Benign according to our data. Variant chr3-49375563-C-T is described in ClinVar as [Benign]. Clinvar id is 720567.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.382 with no splicing effect.
BS2
?
High AC in GnomAd at 382 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHOA | NM_001664.4 | c.27G>A | p.Val9= | synonymous_variant | 2/5 | ENST00000418115.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHOA | ENST00000418115.6 | c.27G>A | p.Val9= | synonymous_variant | 2/5 | 1 | NM_001664.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00251 AC: 382AN: 152186Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.000737 AC: 185AN: 250848Hom.: 3 AF XY: 0.000649 AC XY: 88AN XY: 135620
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GnomAD4 exome AF: 0.000263 AC: 385AN: 1461384Hom.: 1 Cov.: 31 AF XY: 0.000250 AC XY: 182AN XY: 727002
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GnomAD4 genome ? AF: 0.00251 AC: 383AN: 152304Hom.: 5 Cov.: 31 AF XY: 0.00247 AC XY: 184AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at