rs3803981
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018993.4(RIN2):c.589T>A(p.Ser197Thr) variant causes a missense change. The variant allele was found at a frequency of 0.153 in 1,612,492 control chromosomes in the GnomAD database, including 19,608 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S197L) has been classified as Uncertain significance.
Frequency
Consequence
NM_018993.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIN2 | NM_018993.4 | c.589T>A | p.Ser197Thr | missense_variant | 8/13 | ENST00000255006.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIN2 | ENST00000255006.12 | c.589T>A | p.Ser197Thr | missense_variant | 8/13 | 2 | NM_018993.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22859AN: 152048Hom.: 1767 Cov.: 32
GnomAD3 exomes AF: 0.152 AC: 37812AN: 247982Hom.: 3152 AF XY: 0.149 AC XY: 19980AN XY: 134464
GnomAD4 exome AF: 0.153 AC: 223428AN: 1460326Hom.: 17843 Cov.: 31 AF XY: 0.151 AC XY: 109484AN XY: 726396
GnomAD4 genome ? AF: 0.150 AC: 22866AN: 152166Hom.: 1765 Cov.: 32 AF XY: 0.150 AC XY: 11163AN XY: 74398
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 11, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at