rs5859
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004261.5(SELENOF):c.*632G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,382 control chromosomes in the GnomAD database, including 9,394 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 9390 hom., cov: 33)
Exomes 𝑓: 0.22 ( 4 hom. )
Consequence
SELENOF
NM_004261.5 3_prime_UTR
NM_004261.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.628
Genes affected
SELENOF (HGNC:17705): (selenoprotein F) The protein encoded by this gene belongs to the SEP15/selenoprotein M family. The exact function of this protein is not known; however, it has been found to associate with UDP-glucose:glycoprotein glucosyltransferase (UGTR), an endoplasmic reticulum(ER)-resident protein, which is involved in the quality control of protein folding. The association with UGTR retains this protein in the ER, where it may play a role in protein folding. It has also been suggested to have a role in cancer etiology. This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELENOF | NM_004261.5 | c.*632G>A | 3_prime_UTR_variant | 5/5 | ENST00000331835.10 | NP_004252.2 | ||
SELENOF | NM_203341.3 | c.*705G>A | 3_prime_UTR_variant | 4/4 | NP_976086.1 | |||
SELENOF | NR_144512.1 | n.1207G>A | non_coding_transcript_exon_variant | 5/5 | ||||
SELENOF | NR_144513.1 | n.1191G>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELENOF | ENST00000331835.10 | c.*632G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_004261.5 | ENSP00000328729.6 | |||
SELENOF | ENST00000370554.5 | c.*705G>A | 3_prime_UTR_variant | 4/4 | 1 | ENSP00000359585.2 | ||||
SELENOF | ENST00000648872.1 | n.*847G>A | non_coding_transcript_exon_variant | 6/6 | ENSP00000497584.1 | |||||
SELENOF | ENST00000648872.1 | n.*847G>A | 3_prime_UTR_variant | 6/6 | ENSP00000497584.1 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 46409AN: 151930Hom.: 9366 Cov.: 33
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GnomAD4 exome AF: 0.222 AC: 74AN: 334Hom.: 4 Cov.: 0 AF XY: 0.227 AC XY: 45AN XY: 198
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GnomAD4 genome AF: 0.306 AC: 46498AN: 152048Hom.: 9390 Cov.: 33 AF XY: 0.299 AC XY: 22210AN XY: 74330
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at