rs112284414
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_030930.4(UNC93B1):āc.1206G>Cā(p.Pro402=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,547,488 control chromosomes in the GnomAD database, including 511 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.026 ( 139 hom., cov: 29)
Exomes š: 0.010 ( 372 hom. )
Consequence
UNC93B1
NM_030930.4 synonymous
NM_030930.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.812
Genes affected
UNC93B1 (HGNC:13481): (unc-93 homolog B1, TLR signaling regulator) This gene encodes a protein that is involved in innate and adaptive immune response by regulating toll-like receptor signaling. The encoded protein traffics nucleotide sensing toll-like receptors to the endolysosome from the endoplasmic reticulum. Deficiency of the encoded protein has been associated with herpes simplex encephalitis. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 11-67995768-C-G is Benign according to our data. Variant chr11-67995768-C-G is described in ClinVar as [Benign]. Clinvar id is 470489.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.812 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UNC93B1 | NM_030930.4 | c.1206G>C | p.Pro402= | synonymous_variant | 9/11 | ENST00000227471.7 | NP_112192.2 | |
UNC93B1 | XM_011545290.1 | c.795G>C | p.Pro265= | synonymous_variant | 7/9 | XP_011543592.1 | ||
UNC93B1 | XM_011545291.3 | c.651G>C | p.Pro217= | synonymous_variant | 6/8 | XP_011543593.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UNC93B1 | ENST00000227471.7 | c.1206G>C | p.Pro402= | synonymous_variant | 9/11 | 1 | NM_030930.4 | ENSP00000227471 | P1 | |
UNC93B1 | ENST00000525368.1 | n.213G>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0262 AC: 3975AN: 151758Hom.: 138 Cov.: 29
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GnomAD3 exomes AF: 0.0182 AC: 2736AN: 149964Hom.: 87 AF XY: 0.0213 AC XY: 1718AN XY: 80652
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GnomAD4 exome AF: 0.0104 AC: 14518AN: 1395612Hom.: 372 Cov.: 36 AF XY: 0.0120 AC XY: 8257AN XY: 688416
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GnomAD4 genome AF: 0.0263 AC: 3999AN: 151876Hom.: 139 Cov.: 29 AF XY: 0.0261 AC XY: 1940AN XY: 74228
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
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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