chr19-38870121-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001195833.2(RINL):c.1164G>A(p.Gly388=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,421,752 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00046 ( 4 hom. )
Consequence
RINL
NM_001195833.2 synonymous
NM_001195833.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.929
Genes affected
RINL (HGNC:24795): (Ras and Rab interactor like) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in endocytosis. Predicted to be located in actin cytoskeleton and ruffle. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.42).
BP6
?
Variant 19-38870121-C-T is Benign according to our data. Variant chr19-38870121-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649823.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.929 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RINL | NM_001195833.2 | c.1164G>A | p.Gly388= | synonymous_variant | 9/12 | ENST00000591812.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINL | ENST00000591812.2 | c.1164G>A | p.Gly388= | synonymous_variant | 9/12 | 2 | NM_001195833.2 | P2 | |
RINL | ENST00000598904.5 | c.822G>A | p.Gly274= | synonymous_variant | 8/11 | 5 | A2 | ||
RINL | ENST00000589111.5 | n.1631G>A | non_coding_transcript_exon_variant | 6/9 | 2 | ||||
ENST00000593830.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152202Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00152 AC: 42AN: 27584Hom.: 0 AF XY: 0.00223 AC XY: 37AN XY: 16620
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GnomAD4 exome AF: 0.000461 AC: 585AN: 1269442Hom.: 4 Cov.: 34 AF XY: 0.000593 AC XY: 369AN XY: 622076
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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 | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | RINL: BP4, BP7 - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at