X-143629567-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001184749.3(SLITRK4):c.1542C>T(p.Ser514Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.87 ( 30818 hom., 28193 hem., cov: 22)
Exomes 𝑓: 0.99 ( 357894 hom. 359386 hem. )
Failed GnomAD Quality Control
Consequence
SLITRK4
NM_001184749.3 synonymous
NM_001184749.3 synonymous
Scores
1
Clinical Significance
Conservation
PhyloP100: 0.0630
Genes affected
SLITRK4 (HGNC:23502): (SLIT and NTRK like family member 4) This gene encodes a transmembrane protein belonging to the the SLITRK family. These family members include two N-terminal leucine-rich repeat domains similar to those found in the axonal growth-controlling protein SLIT, as well as C-terminal regions similar to neurotrophin receptors. Studies of an homologous protein in mouse suggest that this family member functions to suppress neurite outgrowth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant X-143629567-G-A is Benign according to our data. Variant chrX-143629567-G-A is described in ClinVar as [Benign]. Clinvar id is 769233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.063 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLITRK4 | ENST00000356928.2 | c.1542C>T | p.Ser514Ser | synonymous_variant | Exon 2 of 2 | 2 | NM_001184749.3 | ENSP00000349400.1 | ||
SLITRK4 | ENST00000338017.8 | c.1542C>T | p.Ser514Ser | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000336627.4 | |||
SLITRK4 | ENST00000596188.2 | c.1542C>T | p.Ser514Ser | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000469205.1 |
Frequencies
GnomAD3 genomes AF: 0.872 AC: 95698AN: 109752Hom.: 30823 Cov.: 22 AF XY: 0.880 AC XY: 28150AN XY: 31988
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.986 AC: 1082492AN: 1098252Hom.: 357894 Cov.: 65 AF XY: 0.988 AC XY: 359386AN XY: 363606
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.872 AC: 95731AN: 109801Hom.: 30818 Cov.: 22 AF XY: 0.880 AC XY: 28193AN XY: 32047
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 16, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at