1-86863481-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004261.5(SELENOF):c.491G>A(p.Arg164His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000227 in 1,610,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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. R164C) has been classified as Uncertain significance.
Frequency
Consequence
NM_004261.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOF | NM_004261.5 | c.491G>A | p.Arg164His | missense_variant | 5/5 | ENST00000331835.10 | |
SELENOF | NM_203341.3 | c.*66G>A | 3_prime_UTR_variant | 4/4 | |||
SELENOF | NR_144512.1 | n.568G>A | non_coding_transcript_exon_variant | 5/5 | |||
SELENOF | NR_144513.1 | n.552G>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOF | ENST00000331835.10 | c.491G>A | p.Arg164His | missense_variant | 5/5 | 1 | NM_004261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000691 AC: 17AN: 246002Hom.: 0 AF XY: 0.0000674 AC XY: 9AN XY: 133434
GnomAD4 exome AF: 0.000235 AC: 343AN: 1458640Hom.: 0 Cov.: 30 AF XY: 0.000218 AC XY: 158AN XY: 725550
GnomAD4 genome AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.491G>A (p.R164H) alteration is located in exon 5 (coding exon 5) of the SEP15 gene. This alteration results from a G to A substitution at nucleotide position 491, causing the arginine (R) at amino acid position 164 to be replaced by a histidine (H). 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