chr3-89342064-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005233.6(EPHA3):c.1280C>T(p.Ala427Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000621 in 1,610,266 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A427A) has been classified as Likely benign.
Frequency
Consequence
NM_005233.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA3 | NM_005233.6 | c.1280C>T | p.Ala427Val | missense_variant | 5/17 | ENST00000336596.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA3 | ENST00000336596.7 | c.1280C>T | p.Ala427Val | missense_variant | 5/17 | 1 | NM_005233.6 | P1 | |
EPHA3 | ENST00000494014.1 | c.1280C>T | p.Ala427Val | missense_variant | 5/17 | 1 | |||
EPHA3 | ENST00000452448.6 | c.1280C>T | p.Ala427Val | missense_variant | 5/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000673 AC: 1AN: 148550Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248908Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134702
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461598Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727082
GnomAD4 genome ? AF: 0.00000673 AC: 1AN: 148668Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.1280C>T (p.A427V) alteration is located in exon 5 (coding exon 5) of the EPHA3 gene. This alteration results from a C to T substitution at nucleotide position 1280, causing the alanine (A) at amino acid position 427 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at