chr3-96814728-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001080448.3(EPHA6):c.105C>G(p.Cys35Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000444 in 1,576,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPHA6 | NM_001080448.3 | c.105C>G | p.Cys35Trp | missense_variant | Exon 1 of 18 | ENST00000389672.10 | NP_001073917.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHA6 | ENST00000389672.10 | c.105C>G | p.Cys35Trp | missense_variant | Exon 1 of 18 | 1 | NM_001080448.3 | ENSP00000374323.5 | ||
EPHA6 | ENST00000470610.6 | c.105C>G | p.Cys35Trp | missense_variant | Exon 1 of 5 | 2 | ENSP00000420598.2 | |||
EPHA6 | ENST00000506569.1 | c.-64C>G | upstream_gene_variant | 1 | ENSP00000425132.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000185 AC: 4AN: 216096Hom.: 0 AF XY: 0.0000254 AC XY: 3AN XY: 118182
GnomAD4 exome AF: 0.00000351 AC: 5AN: 1424584Hom.: 0 Cov.: 35 AF XY: 0.00000425 AC XY: 3AN XY: 705328
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.105C>G (p.C35W) alteration is located in exon 1 (coding exon 1) of the EPHA6 gene. This alteration results from a C to G substitution at nucleotide position 105, causing the cysteine (C) at amino acid position 35 to be replaced by a tryptophan (W). 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