dbSNP rs112284414: UNC93B1:p.Pro402Pro (chr11-67995768-C-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_030930.4(UNC93B1):c.1206G>C(p.Pro402Pro) 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 (★★).

Frequency

Genomes: 𝑓 0.026 ( 139 hom., cov: 29)

Exomes 𝑓: 0.010 ( 372 hom. )

Consequence

UNC93B1
NM_030930.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

UNC93B1 links:

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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 rank	MANE	Protein	UniProt
UNC93B1	NM_030930.4 link	c.1206G>C	p.Pro402Pro	synonymous_variant	Exon 9 of 11	ENST00000227471.7	NP_112192.2	Q9H1C4
UNC93B1	XM_011545290.1 link	c.795G>C	p.Pro265Pro	synonymous_variant	Exon 7 of 9		XP_011543592.1
UNC93B1	XM_011545291.3 link	c.651G>C	p.Pro217Pro	synonymous_variant	Exon 6 of 8		XP_011543593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC93B1	ENST00000227471.7 link	c.1206G>C	p.Pro402Pro	synonymous_variant	Exon 9 of 11	1	NM_030930.4	ENSP00000227471.3		Q9H1C4
UNC93B1	ENST00000525368.1 link	n.213G>C		non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3975

AN:

151758

Hom.:

138

Cov.:

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.:

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.:

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

AF:

0.0263

AC:

3999

AN:

151876

Hom.:

139

Cov.:

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.:

Bravo

AF:

0.0273

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over