4-25159110-TAAA-TA
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_016955.4(SEPSECS):c.115-5_115-4delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000706 in 1,456,956 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.000057 ( 0 hom., cov: 26)
Exomes 𝑓: 0.00078 ( 0 hom. )
Consequence
SEPSECS
NM_016955.4 splice_region, intron
NM_016955.4 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.13
Genes affected
SEPSECS (HGNC:30605): (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) The amino acid selenocysteine is the only amino acid that does not have its own tRNA synthetase. Instead, this amino acid is synthesized on its cognate tRNA in a three step process. The protein encoded by this gene catalyzes the third step in the process, the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 4-25159110-TAA-T is Benign according to our data. Variant chr4-25159110-TAA-T is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEPSECS | NM_016955.4 | c.115-5_115-4delTT | splice_region_variant, intron_variant | ENST00000382103.7 | NP_058651.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEPSECS | ENST00000382103.7 | c.115-5_115-4delTT | splice_region_variant, intron_variant | 1 | NM_016955.4 | ENSP00000371535.2 |
Frequencies
GnomAD3 genomes AF: 0.0000567 AC: 8AN: 141122Hom.: 0 Cov.: 26
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GnomAD4 exome AF: 0.000775 AC: 1020AN: 1315834Hom.: 0 AF XY: 0.000784 AC XY: 513AN XY: 654306
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GnomAD4 genome AF: 0.0000567 AC: 8AN: 141122Hom.: 0 Cov.: 26 AF XY: 0.0000878 AC XY: 6AN XY: 68324
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at