chr1-154582078-G-GT
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_001111.5(ADAR):c.*2727_*2728insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00291 in 149,016 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0029 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0047 ( 0 hom. )
Consequence
ADAR
NM_001111.5 3_prime_UTR
NM_001111.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.124
Genes affected
ADAR (HGNC:225): (adenosine deaminase RNA specific) This gene encodes the enzyme responsible for RNA editing by site-specific deamination of adenosines. This enzyme destabilizes double-stranded RNA through conversion of adenosine to inosine. Mutations in this gene have been associated with dyschromatosis symmetrica hereditaria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0029 (431/148590) while in subpopulation AFR AF= 0.00765 (310/40510). AF 95% confidence interval is 0.00695. There are 2 homozygotes in gnomad4. There are 206 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAd4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAR | NM_001111.5 | c.*2727_*2728insA | 3_prime_UTR_variant | 15/15 | ENST00000368474.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAR | ENST00000368474.9 | c.*2727_*2728insA | 3_prime_UTR_variant | 15/15 | 1 | NM_001111.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00290 AC: 430AN: 148498Hom.: 2 Cov.: 31
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GnomAD4 exome AF: 0.00469 AC: 2AN: 426Hom.: 0 Cov.: 0 AF XY: 0.00391 AC XY: 1AN XY: 256
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GnomAD4 genome AF: 0.00290 AC: 431AN: 148590Hom.: 2 Cov.: 31 AF XY: 0.00284 AC XY: 206AN XY: 72450
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Symmetrical dyschromatosis of extremities Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at