chr6-71887051-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_014989.7(RIMS1):c.28C>T(p.Pro10Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000134 in 1,613,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P10R) has been classified as Uncertain significance.
Frequency
Consequence
NM_014989.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIMS1 | NM_014989.7 | c.28C>T | p.Pro10Ser | missense_variant | 1/34 | ENST00000521978.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIMS1 | ENST00000521978.6 | c.28C>T | p.Pro10Ser | missense_variant | 1/34 | 1 | NM_014989.7 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 58AN: 246404Hom.: 0 AF XY: 0.000209 AC XY: 28AN XY: 134112
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461122Hom.: 0 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 726810
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 21, 2016 | - - |
Cone-rod dystrophy 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at