chr20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGACACT
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM4BP6_Moderate
The NM_152503.8(MROH8):c.92+1_93insAGTGTCGGCCGCGGGGCCCTGTCTGTAAG(p.Asn31LysfsTer10) variant causes a splice donor, stop gained, frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MROH8
NM_152503.8 splice_donor, stop_gained, frameshift
NM_152503.8 splice_donor, stop_gained, frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.659
Genes affected
MROH8 (HGNC:16125): (maestro heat like repeat family member 8) The protein encoded by this gene belongs to the maestro heat-like repeat family. The exact function of this gene is not known, however, in a genome-wide association study using hippocampal atrophy as a quantitative trait, this gene has been associated with Alzheimer's disease (PMID:19668339). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
RPN2 (HGNC:10382): (ribophorin II) This gene encodes a type I integral membrane protein found only in the rough endoplasmic reticulum. The encoded protein is part of an N-oligosaccharyl transferase complex that links high mannose oligosaccharides to asparagine residues found in the Asn-X-Ser/Thr consensus motif of nascent polypeptide chains. This protein is similar in sequence to the yeast oligosaccharyl transferase subunit SWP1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM4
?
Stoplost variant in NM_152503.8 Downstream stopcodon found after 781 codons.
BP6
?
Variant 20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGACACT is Benign according to our data. Variant chr20-37179387-G-GCTTACAGACAGGGCCCCGCGGCCGACACT is described in ClinVar as [Likely_benign]. Clinvar id is 1986160.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MROH8 | NM_152503.8 | c.92+1_93insAGTGTCGGCCGCGGGGCCCTGTCTGTAAG | p.Asn31LysfsTer10 | splice_donor_variant, stop_gained, frameshift_variant | ENST00000710289.2 | ||
RPN2 | NM_002951.5 | c.13+21_13+22insACAGACAGGGCCCCGCGGCCGACACTCTT | intron_variant | ENST00000237530.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MROH8 | ENST00000343811.10 | c.92+1_93insAGTGTCGGCCGCGGGGCCCTGTCTGTAAG | p.Asn31LysfsTer10 | splice_donor_variant, stop_gained, frameshift_variant | 1 | P2 | |||
RPN2 | ENST00000237530.11 | c.13+21_13+22insACAGACAGGGCCCCGCGGCCGACACTCTT | intron_variant | 1 | NM_002951.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1355844Hom.: 0 Cov.: 83 AF XY: 0.00 AC XY: 0AN XY: 663772
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1355844
Hom.:
Cov.:
83
AF XY:
AC XY:
0
AN XY:
663772
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GnomAD4 genome ? Cov.: 0
GnomAD4 genome
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Cov.:
0
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Computational scores
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Name
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at