chr19-38871120-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.559C>T(p.Pro187Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,611,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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.559C>T | p.Pro187Ser | missense_variant | 7/12 | ENST00000591812.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINL | ENST00000591812.2 | c.559C>T | p.Pro187Ser | missense_variant | 7/12 | 2 | NM_001195833.2 | P2 | |
ENST00000593830.1 | n.291+306G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
RINL | ENST00000598904.5 | c.217C>T | p.Pro73Ser | missense_variant | 6/11 | 5 | A2 | ||
RINL | ENST00000589111.5 | n.1026C>T | non_coding_transcript_exon_variant | 4/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248358Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134280
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459602Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726134
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.559C>T (p.P187S) alteration is located in exon 7 (coding exon 6) of the RINL gene. This alteration results from a C to T substitution at nucleotide position 559, causing the proline (P) at amino acid position 187 to be replaced by a serine (S). 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