chr2-221426155-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004438.5(EPHA4):c.2847-13G>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 0.0000797 in 1,606,412 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 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000080 ( 0 hom. )
Consequence
EPHA4
NM_004438.5 splice_polypyrimidine_tract, intron
NM_004438.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.870
Genes affected
EPHA4 (HGNC:3388): (EPH receptor A4) This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 2-221426155-C-T is Benign according to our data. Variant chr2-221426155-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1645204.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA4 | NM_004438.5 | c.2847-13G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000281821.7 | |||
EPHA4 | NM_001304536.2 | c.2847-13G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
EPHA4 | NM_001304537.2 | c.2694-13G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
EPHA4 | NM_001363748.2 | c.*26-13G>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA4 | ENST00000281821.7 | c.2847-13G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004438.5 | P1 | |||
EPHA4 | ENST00000409854.5 | c.*26-13G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
EPHA4 | ENST00000409938.5 | c.2847-13G>A | splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 | ||||
EPHA4 | ENST00000424339.1 | c.*151-13G>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000790 AC: 12AN: 151950Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248944Hom.: 0 AF XY: 0.000112 AC XY: 15AN XY: 134446
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GnomAD4 exome AF: 0.0000798 AC: 116AN: 1454344Hom.: 0 Cov.: 29 AF XY: 0.000101 AC XY: 73AN XY: 723892
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GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
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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 | Sep 26, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at