9-84001057-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001358291.2(RMI1):c.71C>T(p.Pro24Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,613,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001358291.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RMI1 | NM_001358291.2 | c.71C>T | p.Pro24Leu | missense_variant | Exon 3 of 3 | ENST00000445877.6 | NP_001345220.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RMI1 | ENST00000445877.6 | c.71C>T | p.Pro24Leu | missense_variant | Exon 3 of 3 | 1 | NM_001358291.2 | ENSP00000402433.2 | ||
RMI1 | ENST00000325875.7 | c.71C>T | p.Pro24Leu | missense_variant | Exon 3 of 3 | 2 | ENSP00000317039.3 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152064Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251134Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135734
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461718Hom.: 0 Cov.: 33 AF XY: 0.0000633 AC XY: 46AN XY: 727160
GnomAD4 genome AF: 0.000289 AC: 44AN: 152064Hom.: 1 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74268
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at