15-48996449-A-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000559471.6(SECISBP2L):c.2541T>A(p.Ser847=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,832 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
SECISBP2L
ENST00000559471.6 synonymous
ENST00000559471.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.143
Genes affected
SECISBP2L (HGNC:28997): (SECIS binding protein 2 like) Enables RNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 15-48996449-A-T is Benign according to our data. Variant chr15-48996449-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 745125.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.143 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SECISBP2L | NM_001193489.2 | c.2541T>A | p.Ser847= | synonymous_variant | 17/18 | ENST00000559471.6 | NP_001180418.1 | |
SECISBP2L | NM_014701.4 | c.2406T>A | p.Ser802= | synonymous_variant | 16/17 | NP_055516.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SECISBP2L | ENST00000559471.6 | c.2541T>A | p.Ser847= | synonymous_variant | 17/18 | 1 | NM_001193489.2 | ENSP00000453854 | P4 | |
SECISBP2L | ENST00000261847.7 | c.2406T>A | p.Ser802= | synonymous_variant | 16/17 | 1 | ENSP00000261847 | A1 | ||
SECISBP2L | ENST00000380927.6 | c.1827T>A | p.Ser609= | synonymous_variant | 17/17 | 1 | ENSP00000370314 | |||
SECISBP2L | ENST00000561428.1 | c.42T>A | p.Ser14= | synonymous_variant | 1/3 | 3 | ENSP00000454144 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727216
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1461832
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31
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4
AN XY:
727216
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 21, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
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