1-22576863-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020526.5(EPHA8):c.806G>A(p.Arg269Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,594,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020526.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA8 | NM_020526.5 | c.806G>A | p.Arg269Gln | missense_variant | 3/17 | ENST00000166244.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA8 | ENST00000166244.8 | c.806G>A | p.Arg269Gln | missense_variant | 3/17 | 2 | NM_020526.5 | P1 | |
EPHA8 | ENST00000374644.8 | c.806G>A | p.Arg269Gln | missense_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000929 AC: 22AN: 236734Hom.: 0 AF XY: 0.0000933 AC XY: 12AN XY: 128582
GnomAD4 exome AF: 0.0000277 AC: 40AN: 1442472Hom.: 0 Cov.: 32 AF XY: 0.0000210 AC XY: 15AN XY: 714600
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.806G>A (p.R269Q) alteration is located in exon 3 (coding exon 3) of the EPHA8 gene. This alteration results from a G to A substitution at nucleotide position 806, causing the arginine (R) at amino acid position 269 to be replaced by a glutamine (Q). 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