chr14-92555756-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024832.5(RIN3):āc.50T>Cā(p.Val17Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,613,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024832.5 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 |
---|---|---|---|---|---|---|---|
RIN3 | NM_024832.5 | c.50T>C | p.Val17Ala | missense_variant | 2/10 | ENST00000216487.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIN3 | ENST00000216487.12 | c.50T>C | p.Val17Ala | missense_variant | 2/10 | 1 | NM_024832.5 | P2 | |
RIN3 | ENST00000555589.5 | c.50T>C | p.Val17Ala | missense_variant, NMD_transcript_variant | 2/9 | 1 | |||
RIN3 | ENST00000620541.4 | c.50T>C | p.Val17Ala | missense_variant | 2/11 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251356Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135850
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 727220
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at