chr1-86914090-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004261.5(SELENOF):āc.22C>Gā(p.Pro8Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P8S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004261.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOF | NM_004261.5 | c.22C>G | p.Pro8Ala | missense_variant | 1/5 | ENST00000331835.10 | |
SELENOF | NM_203341.3 | c.22C>G | p.Pro8Ala | missense_variant | 1/4 | ||
SELENOF | NR_144512.1 | n.161+225C>G | intron_variant, non_coding_transcript_variant | ||||
SELENOF | NR_144513.1 | n.145+343C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOF | ENST00000331835.10 | c.22C>G | p.Pro8Ala | missense_variant | 1/5 | 1 | NM_004261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 248978Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135136
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727128
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.22C>G (p.P8A) alteration is located in exon 1 (coding exon 1) of the SEP15 gene. This alteration results from a C to G substitution at nucleotide position 22, causing the proline (P) at amino acid position 8 to be replaced by an alanine (A). 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