1-228157753-G-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_020435.4(GJC2):c.-6G>C variant causes a 5 prime UTR change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.30 ( 0 hom., cov: 0)
Exomes 𝑓: 0.18 ( 489 hom. )
Failed GnomAD Quality Control
Consequence
GJC2
NM_020435.4 5_prime_UTR
NM_020435.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.69
Genes affected
GJC2 (HGNC:17494): (gap junction protein gamma 2) This gene encodes a gap junction protein. Gap junction proteins are members of a large family of homologous connexins and comprise 4 transmembrane, 2 extracellular, and 3 cytoplasmic domains. This gene plays a key role in central myelination and is involved in peripheral myelination in humans. Defects in this gene are the cause of autosomal recessive Pelizaeus-Merzbacher-like disease-1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 1-228157753-G-C is Benign according to our data. Variant chr1-228157753-G-C is described in ClinVar as [Benign]. Clinvar id is 402902.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJC2 | NM_020435.4 | c.-6G>C | 5_prime_UTR_variant | 2/2 | ENST00000366714.3 | NP_065168.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9189AN: 30906Hom.: 0 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.446 AC: 36862AN: 82652Hom.: 38 AF XY: 0.446 AC XY: 19544AN XY: 43866
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.180 AC: 98728AN: 549468Hom.: 489 Cov.: 19 AF XY: 0.192 AC XY: 53456AN XY: 278490
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.297 AC: 9189AN: 30890Hom.: 0 Cov.: 0 AF XY: 0.271 AC XY: 4186AN XY: 15474
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at