chr19-38870207-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001195833.2(RINL):c.1078G>A(p.Ala360Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,389,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001195833.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RINL | NM_001195833.2 | c.1078G>A | p.Ala360Thr | missense_variant | 9/12 | ENST00000591812.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINL | ENST00000591812.2 | c.1078G>A | p.Ala360Thr | missense_variant | 9/12 | 2 | NM_001195833.2 | P2 | |
ENST00000593830.1 | n.49C>T | non_coding_transcript_exon_variant | 1/3 | 3 | |||||
RINL | ENST00000598904.5 | c.736G>A | p.Ala246Thr | missense_variant | 8/11 | 5 | A2 | ||
RINL | ENST00000589111.5 | n.1545G>A | non_coding_transcript_exon_variant | 6/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152202Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000171 AC: 212AN: 1237748Hom.: 0 Cov.: 34 AF XY: 0.000151 AC XY: 91AN XY: 601158
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2022 | The c.1078G>A (p.A360T) alteration is located in exon 9 (coding exon 8) of the RINL gene. This alteration results from a G to A substitution at nucleotide position 1078, causing the alanine (A) at amino acid position 360 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at