6-93258245-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004440.4(EPHA7):āc.1964C>Gā(p.Pro655Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,610,332 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P655A) has been classified as Uncertain significance.
Frequency
Consequence
NM_004440.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA7 | NM_004440.4 | c.1964C>G | p.Pro655Arg | missense_variant | 11/17 | ENST00000369303.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA7 | ENST00000369303.9 | c.1964C>G | p.Pro655Arg | missense_variant | 11/17 | 1 | NM_004440.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458466Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 2AN XY: 725216
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.1964C>G (p.P655R) alteration is located in exon 11 (coding exon 11) of the EPHA7 gene. This alteration results from a C to G substitution at nucleotide position 1964, causing the proline (P) at amino acid position 655 to be replaced by an arginine (R). 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