chr10-1233818-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_018702.4(ADARB2):c.1389G>A(p.Ser463=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,613,988 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 20 hom., cov: 30)
Exomes 𝑓: 0.00086 ( 9 hom. )
Consequence
ADARB2
NM_018702.4 synonymous
NM_018702.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.940
Genes affected
ADARB2 (HGNC:227): (adenosine deaminase RNA specific B2 (inactive)) This gene encodes a member of the double-stranded RNA adenosine deaminase family of RNA-editing enzymes and may play a regulatory role in RNA editing. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 10-1233818-C-T is Benign according to our data. Variant chr10-1233818-C-T is described in ClinVar as [Benign]. Clinvar id is 789439.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.94 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00623 (948/152170) while in subpopulation AFR AF= 0.0213 (883/41484). AF 95% confidence interval is 0.0201. There are 20 homozygotes in gnomad4. There are 442 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADARB2 | NM_018702.4 | c.1389G>A | p.Ser463= | synonymous_variant | 6/10 | ENST00000381312.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADARB2 | ENST00000381312.6 | c.1389G>A | p.Ser463= | synonymous_variant | 6/10 | 1 | NM_018702.4 | P1 | |
LINC00200 | ENST00000655745.1 | n.265-54655C>T | intron_variant, non_coding_transcript_variant | ||||||
ADARB2 | ENST00000469464.1 | n.173G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00622 AC: 946AN: 152052Hom.: 20 Cov.: 30
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GnomAD3 exomes AF: 0.00209 AC: 526AN: 251360Hom.: 5 AF XY: 0.00156 AC XY: 212AN XY: 135852
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GnomAD4 exome AF: 0.000864 AC: 1263AN: 1461818Hom.: 9 Cov.: 33 AF XY: 0.000769 AC XY: 559AN XY: 727204
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GnomAD4 genome ? AF: 0.00623 AC: 948AN: 152170Hom.: 20 Cov.: 30 AF XY: 0.00594 AC XY: 442AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2018 | - - |
Computational scores
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BayesDel_noAF
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