5-122066764-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_002317.7(LOX):c.1248-15G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000589 in 1,528,672 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: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000058 ( 0 hom. )
Consequence
LOX
NM_002317.7 splice_polypyrimidine_tract, intron
NM_002317.7 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.298
Genes affected
LOX (HGNC:6664): (lysyl oxidase) This gene encodes a member of the lysyl oxidase family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate a regulatory propeptide and the mature enzyme. The copper-dependent amine oxidase activity of this enzyme functions in the crosslinking of collagens and elastin, while the propeptide may play a role in tumor suppression. In addition, defects in this gene have been linked with predisposition to thoracic aortic aneurysms and dissections. [provided by RefSeq, Jul 2016]
SRFBP1 (HGNC:26333): (serum response factor binding protein 1) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA. Predicted to be located in perinuclear region of cytoplasm. Predicted to be part of 90S preribosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 5-122066764-C-T is Benign according to our data. Variant chr5-122066764-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2997980.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOX | NM_002317.7 | c.1248-15G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000231004.5 | |||
LOX | NM_001178102.2 | c.558-15G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
LOX | NM_001317073.1 | c.357-15G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
SRFBP1 | XM_017009111.3 | c.1106-8551C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOX | ENST00000231004.5 | c.1248-15G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002317.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151928Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000581 AC: 8AN: 1376744Hom.: 0 Cov.: 22 AF XY: 0.00000724 AC XY: 5AN XY: 690206
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151928Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74198
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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 | Invitae | Aug 29, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at