3-96987441-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001080448.3(EPHA6):c.562C>T(p.Arg188Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000307 in 1,613,726 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPHA6 | NM_001080448.3 | c.562C>T | p.Arg188Cys | 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.562C>T | p.Arg188Cys | missense_variant | Exon 3 of 18 | 1 | NM_001080448.3 | ENSP00000374323.5 | ||
EPHA6 | ENST00000506569.1 | c.394C>T | p.Arg132Cys | missense_variant | Exon 3 of 4 | 1 | ENSP00000425132.1 | |||
EPHA6 | ENST00000470610.6 | c.562C>T | p.Arg188Cys | missense_variant | Exon 3 of 5 | 2 | ENSP00000420598.2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 30AN: 248960Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 135042
GnomAD4 exome AF: 0.000323 AC: 472AN: 1461652Hom.: 0 Cov.: 32 AF XY: 0.000301 AC XY: 219AN XY: 727106
GnomAD4 genome AF: 0.000158 AC: 24AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.562C>T (p.R188C) 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 562, causing the arginine (R) at amino acid position 188 to be replaced by a cysteine (C). 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