6-169773059-A-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018341.3(ERMARD):c.1234-260A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000529 in 378,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000044 ( 0 hom. )
Consequence
ERMARD
NM_018341.3 intron
NM_018341.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.63
Genes affected
ERMARD (HGNC:21056): (ER membrane associated RNA degradation) The protein encoded by this gene contains 2 transmembrane domains near the C-terminus and is localized in the endoplasmic reticulum. Knockout of this gene in developing rat brain showed that it may be involved in neuronal migration. Mutations in this gene are associated with periventricular nodular heterotopia-6 (PVNH6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERMARD | NM_018341.3 | c.1234-260A>T | intron_variant | ENST00000366773.8 | NP_060811.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERMARD | ENST00000366773.8 | c.1234-260A>T | intron_variant | 2 | NM_018341.3 | ENSP00000355735.3 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151346Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000441 AC: 1AN: 226808Hom.: 0 Cov.: 0 AF XY: 0.00000863 AC XY: 1AN XY: 115836
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GnomAD4 genome AF: 0.00000661 AC: 1AN: 151346Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73806
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at