chr6-7189311-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001003699.4(RREB1):c.414G>A(p.Gly138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000557 in 1,437,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000056 ( 0 hom. )
Consequence
RREB1
NM_001003699.4 synonymous
NM_001003699.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.233
Genes affected
RREB1 (HGNC:10449): (ras responsive element binding protein 1) The protein encoded by this gene is a zinc finger transcription factor that binds to RAS-responsive elements (RREs) of gene promoters. It has been shown that the calcitonin gene promoter contains an RRE and that the encoded protein binds there and increases expression of calcitonin, which may be involved in Ras/Raf-mediated cell differentiation. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 6-7189311-G-A is Benign according to our data. Variant chr6-7189311-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 752578.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.233 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RREB1 | NM_001003699.4 | c.414G>A | p.Gly138= | synonymous_variant | 6/13 | ENST00000379938.7 | |
RREB1 | NM_001003698.4 | c.414G>A | p.Gly138= | synonymous_variant | 6/12 | ||
RREB1 | NM_001168344.2 | c.414G>A | p.Gly138= | synonymous_variant | 6/12 | ||
RREB1 | NM_001003700.2 | c.414G>A | p.Gly138= | synonymous_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RREB1 | ENST00000379938.7 | c.414G>A | p.Gly138= | synonymous_variant | 6/13 | 1 | NM_001003699.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000956 AC: 2AN: 209294Hom.: 0 AF XY: 0.00000892 AC XY: 1AN XY: 112140
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GnomAD4 exome AF: 0.00000557 AC: 8AN: 1437164Hom.: 0 Cov.: 30 AF XY: 0.00000421 AC XY: 3AN XY: 712614
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 25, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at