1-228493225-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010858.3(RNF187):c.656C>T(p.Ser219Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,551,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010858.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF187 | ENST00000305943.9 | c.656C>T | p.Ser219Leu | missense_variant | Exon 3 of 4 | 1 | NM_001010858.3 | ENSP00000306396.9 | ||
RNF187 | ENST00000482739.3 | n.534C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000579 AC: 9AN: 155546Hom.: 0 AF XY: 0.0000606 AC XY: 5AN XY: 82498
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1399156Hom.: 0 Cov.: 31 AF XY: 0.0000203 AC XY: 14AN XY: 690096
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.656C>T (p.S219L) alteration is located in exon 3 (coding exon 3) of the RNF187 gene. This alteration results from a C to T substitution at nucleotide position 656, causing the serine (S) at amino acid position 219 to be replaced by a leucine (L). 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