2-42263239-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019063.5(EML4):c.574C>T(p.Arg192Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,612,636 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R192H) has been classified as Uncertain significance.
Frequency
Consequence
NM_019063.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EML4 | ENST00000318522.10 | c.574C>T | p.Arg192Cys | missense_variant | Exon 5 of 23 | 1 | NM_019063.5 | ENSP00000320663.5 | ||
EML4 | ENST00000402711.6 | c.400C>T | p.Arg134Cys | missense_variant | Exon 4 of 22 | 1 | ENSP00000385059.2 | |||
EML4 | ENST00000401738.3 | c.574C>T | p.Arg192Cys | missense_variant | Exon 5 of 24 | 5 | ENSP00000384939.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250742Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135544
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1460636Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 726610
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.574C>T (p.R192C) alteration is located in exon 5 (coding exon 5) of the EML4 gene. This alteration results from a C to T substitution at nucleotide position 574, causing the arginine (R) at amino acid position 192 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