rs796106217
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_030930.4(UNC93B1):c.1071C>T(p.Ala357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000516 in 1,550,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000052 ( 0 hom. )
Consequence
UNC93B1
NM_030930.4 synonymous
NM_030930.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.71
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 11-67996620-G-A is Benign according to our data. Variant chr11-67996620-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 537931.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.71 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC93B1 | NM_030930.4 | c.1071C>T | p.Ala357= | synonymous_variant | 8/11 | ENST00000227471.7 | |
UNC93B1 | XM_011545290.1 | c.660C>T | p.Ala220= | synonymous_variant | 6/9 | ||
UNC93B1 | XM_011545291.3 | c.516C>T | p.Ala172= | synonymous_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC93B1 | ENST00000227471.7 | c.1071C>T | p.Ala357= | synonymous_variant | 8/11 | 1 | NM_030930.4 | P1 | |
UNC93B1 | ENST00000533424.6 | n.1565C>T | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000384 AC: 6AN: 156430Hom.: 0 AF XY: 0.0000605 AC XY: 5AN XY: 82710
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GnomAD4 exome AF: 0.0000522 AC: 73AN: 1398048Hom.: 0 Cov.: 31 AF XY: 0.0000493 AC XY: 34AN XY: 689282
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GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74510
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 18, 2023 | - - |
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