1-74599757-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001002912.5(ERICH3):c.1664G>T(p.Arg555Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R555C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001002912.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERICH3 | NM_001002912.5 | c.1664G>T | p.Arg555Leu | missense_variant | 11/15 | ENST00000326665.10 | |
ERICH3-AS1 | NR_121671.1 | n.81-15449C>A | intron_variant, non_coding_transcript_variant | ||||
ERICH3 | XM_017000275.2 | c.1658G>T | p.Arg553Leu | missense_variant | 11/14 | ||
ERICH3-AS1 | NR_121670.1 | n.173+9850C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERICH3 | ENST00000326665.10 | c.1664G>T | p.Arg555Leu | missense_variant | 11/15 | 5 | NM_001002912.5 | P3 | |
ERICH3 | ENST00000420661.6 | c.1073G>T | p.Arg358Leu | missense_variant | 6/7 | 1 | A2 | ||
ERICH3-AS1 | ENST00000612390.4 | n.81-15449C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
ERICH3-AS1 | ENST00000416017.1 | n.173+9850C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at