chr1-86863482-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004261.5(SELENOF):c.490C>T(p.Arg164Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,611,144 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R164H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004261.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOF | NM_004261.5 | c.490C>T | p.Arg164Cys | missense_variant | 5/5 | ENST00000331835.10 | |
SELENOF | NM_203341.3 | c.*65C>T | 3_prime_UTR_variant | 4/4 | |||
SELENOF | NR_144512.1 | n.567C>T | non_coding_transcript_exon_variant | 5/5 | |||
SELENOF | NR_144513.1 | n.551C>T | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOF | ENST00000331835.10 | c.490C>T | p.Arg164Cys | missense_variant | 5/5 | 1 | NM_004261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000650 AC: 16AN: 246182Hom.: 0 AF XY: 0.0000749 AC XY: 10AN XY: 133566
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1458918Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 725694
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.490C>T (p.R164C) alteration is located in exon 5 (coding exon 5) of the SEP15 gene. This alteration results from a C to T substitution at nucleotide position 490, causing the arginine (R) at amino acid position 164 to be replaced by a cysteine (C). 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