3-96987448-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080448.3(EPHA6):c.569C>T(p.Ala190Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,734 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPHA6 | NM_001080448.3 | c.569C>T | p.Ala190Val | missense_variant | Exon 3 of 18 | ENST00000389672.10 | NP_001073917.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHA6 | ENST00000389672.10 | c.569C>T | p.Ala190Val | missense_variant | Exon 3 of 18 | 1 | NM_001080448.3 | ENSP00000374323.5 | ||
EPHA6 | ENST00000506569.1 | c.401C>T | p.Ala134Val | missense_variant | Exon 3 of 4 | 1 | ENSP00000425132.1 | |||
EPHA6 | ENST00000470610.6 | c.569C>T | p.Ala190Val | missense_variant | Exon 3 of 5 | 2 | ENSP00000420598.2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461656Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727112
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.569C>T (p.A190V) alteration is located in exon 3 (coding exon 3) of the EPHA6 gene. This alteration results from a C to T substitution at nucleotide position 569, causing the alanine (A) at amino acid position 190 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