Genetic Variant LILRB1:c.1813-7G>C (chr19-54636725-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001081637.3(LILRB1):c.1813-7G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 17)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LILRB1
NM_001081637.3 splice_region, intron

Scores

Splicing: ADA: 0.00002243

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.99

Publications

11 publications found

Variant links:

Genes affected

LILRB1 (HGNC:6605): (leukocyte immunoglobulin like receptor B1) This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

LILRB1 links:

LILRB1-AS1 (HGNC:53114): (LILRB1 antisense RNA 1)

LILRB1-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001081637.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LILRB1	NM_001081637.3	MANE Select	c.1813-7G>C	splice_region intron	N/A	NP_001075106.2	A0A087WSV6
LILRB1	NM_001388358.1		c.1813-7G>C	splice_region intron	N/A	NP_001375287.1	A0A087WSV6
LILRB1	NM_001081638.4		c.1810-7G>C	splice_region intron	N/A	NP_001075107.2	A0A087WSX8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LILRB1	ENST00000324602.12	TSL:5 MANE Select	c.1813-7G>C	splice_region intron	N/A	ENSP00000315997.7	A0A087WSV6
LILRB1	ENST00000396315.5	TSL:1	c.1813-7G>C	splice_region intron	N/A	ENSP00000379608.1	A0A087WSV6
LILRB1	ENST00000396327.7	TSL:1	c.1810-7G>C	splice_region intron	N/A	ENSP00000379618.3	A0A087WSX8

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

71396

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00

AC:

AN:

203086

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1122328

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

552248

African (AFR)

AF:

0.00

AC:

AN:

24458

American (AMR)

AF:

0.00

AC:

AN:

34176

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17818

East Asian (EAS)

AF:

0.00

AC:

AN:

15960

South Asian (SAS)

AF:

0.00

AC:

AN:

74140

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35426

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3854

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

874912

Other (OTH)

AF:

0.00

AC:

AN:

41584

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

71396

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

33102

African (AFR)

AF:

0.00

AC:

AN:

17034

American (AMR)

AF:

0.00

AC:

AN:

4770

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2088

East Asian (EAS)

AF:

0.00

AC:

AN:

1946

South Asian (SAS)

AF:

0.00

AC:

AN:

1894

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2968

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

39098

Other (OTH)

AF:

0.00

AC:

AN:

952

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.52

(source)

DANN

Benign

0.43

PhyloP100

-6.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000022

dbscSNV1_RF

Benign

0.014

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over