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rs112284414

chr11-67995768-C-Gchr11-67995768-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_030930.4(UNC93B1):c.1206G>C(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 (★). Synonymous variant affecting the same amino acid position (i.e. P402P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.026 ( 139 hom., cov: 29)
Exomes 𝑓: 0.010 ( 372 hom. )

Consequence

UNC93B1
NM_030930.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.812
Variant links:
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.812 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
UNC93B1NM_030930.4 linkuse as main transcriptc.1206G>C p.Pro402= synonymous_variant 9/11 ENST00000227471.7
UNC93B1XM_011545290.1 linkuse as main transcriptc.795G>C p.Pro265= synonymous_variant 7/9
UNC93B1XM_011545291.3 linkuse as main transcriptc.651G>C p.Pro217= synonymous_variant 6/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UNC93B1ENST00000227471.7 linkuse as main transcriptc.1206G>C p.Pro402= synonymous_variant 9/111 NM_030930.4 P1
UNC93B1ENST00000525368.1 linkuse as main transcriptn.213G>C non_coding_transcript_exon_variant 1/32

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0262
AC:
3975
AN:
151758
Hom.:
138
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0731
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0106
Gnomad ASJ
AF:
0.00519
Gnomad EAS
AF:
0.0259
Gnomad SAS
AF:
0.0710
Gnomad FIN
AF:
0.000189
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00415
Gnomad OTH
AF:
0.0101
GnomAD3 exomes
AF:
0.0182
AC:
2736
AN:
149964
Hom.:
87
AF XY:
0.0213
AC XY:
1718
AN XY:
80652
show subpopulations
Gnomad AFR exome
AF:
0.0723
Gnomad AMR exome
AF:
0.00516
Gnomad ASJ exome
AF:
0.00431
Gnomad EAS exome
AF:
0.0195
Gnomad SAS exome
AF:
0.0688
Gnomad FIN exome
AF:
0.000431
Gnomad NFE exome
AF:
0.00452
Gnomad OTH exome
AF:
0.00979
GnomAD4 exome
AF:
0.0104
AC:
14518
AN:
1395612
Hom.:
372
Cov.:
36
AF XY:
0.0120
AC XY:
8257
AN XY:
688416
show subpopulations
Gnomad4 AFR exome
AF:
0.0767
Gnomad4 AMR exome
AF:
0.00619
Gnomad4 ASJ exome
AF:
0.00513
Gnomad4 EAS exome
AF:
0.0301
Gnomad4 SAS exome
AF:
0.0669
Gnomad4 FIN exome
AF:
0.000353
Gnomad4 NFE exome
AF:
0.00416
Gnomad4 OTH exome
AF:
0.0147
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0263
AC:
3999
AN:
151876
Hom.:
139
Cov.:
29
AF XY:
0.0261
AC XY:
1940
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.0736
Gnomad4 AMR
AF:
0.0106
Gnomad4 ASJ
AF:
0.00519
Gnomad4 EAS
AF:
0.0259
Gnomad4 SAS
AF:
0.0704
Gnomad4 FIN
AF:
0.000189
Gnomad4 NFE
AF:
0.00415
Gnomad4 OTH
AF:
0.00995
Alfa
AF:
0.00392
Hom.:
1
Bravo
AF:
0.0273

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
Cadd
Benign
0.19
Dann
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112284414; hg19: chr11-67763239; API