chr1-86863582-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000370554.5(SELENOF):āc.340A>Gā(p.Ile114Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
ENST00000370554.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOF | NM_004261.5 | c.390A>G | p.Val130= | synonymous_variant | 5/5 | ENST00000331835.10 | |
SELENOF | NM_203341.3 | c.340A>G | p.Ile114Val | missense_variant | 4/4 | ||
SELENOF | NR_144512.1 | n.467A>G | non_coding_transcript_exon_variant | 5/5 | |||
SELENOF | NR_144513.1 | n.451A>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOF | ENST00000331835.10 | c.390A>G | p.Val130= | synonymous_variant | 5/5 | 1 | NM_004261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248730Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134966
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461480Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727026
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at