15-101276591-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018445.6(SELENOS):c.161G>C(p.Arg54Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,548 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R54G) has been classified as Uncertain significance.
Frequency
Consequence
NM_018445.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOS | NM_018445.6 | c.161G>C | p.Arg54Pro | missense_variant | 2/6 | ENST00000526049.6 | |
SELENOS | NM_203472.3 | c.161G>C | p.Arg54Pro | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOS | ENST00000526049.6 | c.161G>C | p.Arg54Pro | missense_variant | 2/6 | 1 | NM_018445.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249006Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135146
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461548Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727058
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.161G>C (p.R54P) alteration is located in exon 2 (coding exon 2) of the VIMP gene. This alteration results from a G to C substitution at nucleotide position 161, causing the arginine (R) at amino acid position 54 to be replaced by a proline (P). 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