chr19-38870947-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195833.2(RINL):c.647C>T(p.Pro216Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000941 in 1,605,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RINL | NM_001195833.2 | c.647C>T | p.Pro216Leu | missense_variant | 8/12 | ENST00000591812.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINL | ENST00000591812.2 | c.647C>T | p.Pro216Leu | missense_variant | 8/12 | 2 | NM_001195833.2 | P2 | |
ENST00000593830.1 | n.291+133G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
RINL | ENST00000598904.5 | c.305C>T | p.Pro102Leu | missense_variant | 7/11 | 5 | A2 | ||
RINL | ENST00000589111.5 | n.1114C>T | non_coding_transcript_exon_variant | 5/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000453 AC: 69AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000865 AC: 21AN: 242642Hom.: 0 AF XY: 0.0000605 AC XY: 8AN XY: 132258
GnomAD4 exome AF: 0.0000564 AC: 82AN: 1453206Hom.: 0 Cov.: 33 AF XY: 0.0000498 AC XY: 36AN XY: 723272
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000484 AC XY: 36AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.647C>T (p.P216L) alteration is located in exon 8 (coding exon 7) of the RINL gene. This alteration results from a C to T substitution at nucleotide position 647, causing the proline (P) at amino acid position 216 to be replaced by a leucine (L). 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