19-38871086-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195833.2(RINL):c.593A>G(p.His198Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000662 in 1,600,106 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.593A>G | p.His198Arg | missense_variant | 7/12 | ENST00000591812.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINL | ENST00000591812.2 | c.593A>G | p.His198Arg | missense_variant | 7/12 | 2 | NM_001195833.2 | P2 | |
ENST00000593830.1 | n.291+272T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
RINL | ENST00000598904.5 | c.251A>G | p.His84Arg | missense_variant | 6/11 | 5 | A2 | ||
RINL | ENST00000589111.5 | n.1060A>G | non_coding_transcript_exon_variant | 4/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000168 AC: 40AN: 237760Hom.: 0 AF XY: 0.000203 AC XY: 26AN XY: 128244
GnomAD4 exome AF: 0.0000677 AC: 98AN: 1447922Hom.: 0 Cov.: 33 AF XY: 0.0000709 AC XY: 51AN XY: 719558
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.593A>G (p.H198R) alteration is located in exon 7 (coding exon 6) of the RINL gene. This alteration results from a A to G substitution at nucleotide position 593, causing the histidine (H) at amino acid position 198 to be replaced by an arginine (R). 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