Variant 11-67997585-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_030930.4(UNC93B1):c.906+90A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,573,126 control chromosomes in the GnomAD database, including 161,817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 25002 hom., cov: 34)

Exomes 𝑓: 0.43 ( 136815 hom. )

Consequence

UNC93B1
NM_030930.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.16

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 11-67997585-T-C is Benign according to our data. Variant chr11-67997585-T-C is described in ClinVar as [Benign]. Clinvar id is 2688062.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
UNC93B1	NM_030930.4 linkuse as main transcript	c.906+90A>G	intron_variant	ENST00000227471.7
UNC93B1	XM_011545290.1 linkuse as main transcript	c.495+90A>G	intron_variant
UNC93B1	XM_011545291.3 linkuse as main transcript	c.351+90A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
UNC93B1	ENST00000227471.7 linkuse as main transcript	c.906+90A>G	intron_variant		1	NM_030930.4	P1
UNC93B1	ENST00000622364.4 linkuse as main transcript	n.994A>G	non_coding_transcript_exon_variant	7/7	2
UNC93B1	ENST00000533424.6 linkuse as main transcript	n.1400+90A>G	intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

81518

AN:

152076

Hom.:

24942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.418

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.500

GnomAD4 exome

AF:

0.431

AC:

612739

AN:

1420932

Hom.:

136815

Cov.:

AF XY:

0.430

AC XY:

302587

AN XY:

704182

show subpopulations

Gnomad4 AFR exome

AF:

0.866

Gnomad4 AMR exome

AF:

0.285

Gnomad4 ASJ exome

AF:

0.468

Gnomad4 EAS exome

AF:

0.390

Gnomad4 SAS exome

AF:

0.390

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.430

Gnomad4 OTH exome

AF:

0.445

GnomAD4 genome

AF:

0.536

AC:

81634

AN:

152194

Hom.:

25002

Cov.:

AF XY:

0.524

AC XY:

39016

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.853

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.460

Gnomad4 EAS

AF:

0.418

Gnomad4 SAS

AF:

0.403

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.433

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.446

Hom.:

23490

Bravo

AF:

0.552

Asia WGS

AF:

0.422

AC:

1469

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 61% of patients studied by a panel of primary immunodeficiencies. Number of patients: 58. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.68

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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