chr2-221426537-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PP2PP3_Moderate
The NM_004438.5(EPHA4):c.2773A>G(p.Met925Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004438.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA4 | NM_004438.5 | c.2773A>G | p.Met925Val | missense_variant | 16/18 | ENST00000281821.7 | |
EPHA4 | NM_001304536.2 | c.2773A>G | p.Met925Val | missense_variant | 17/19 | ||
EPHA4 | NM_001363748.2 | c.2773A>G | p.Met925Val | missense_variant | 16/18 | ||
EPHA4 | NM_001304537.2 | c.2620A>G | p.Met874Val | missense_variant | 15/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA4 | ENST00000281821.7 | c.2773A>G | p.Met925Val | missense_variant | 16/18 | 1 | NM_004438.5 | P1 | |
EPHA4 | ENST00000409854.5 | c.2773A>G | p.Met925Val | missense_variant | 16/17 | 1 | |||
EPHA4 | ENST00000409938.5 | c.2773A>G | p.Met925Val | missense_variant | 17/18 | 2 | P1 | ||
EPHA4 | ENST00000424339.1 | c.*77A>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727210
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.2773A>G (p.M925V) alteration is located in exon 16 (coding exon 16) of the EPHA4 gene. This alteration results from a A to G substitution at nucleotide position 2773, causing the methionine (M) at amino acid position 925 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
Publications
No publications associated with this variant yet.