ENST00000396365.7:c.614G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000396365.7(LILRA6):c.614G>A(p.Arg205Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,255,248 control chromosomes in the GnomAD database, including 46,194 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 4176 hom., cov: 23)

Exomes 𝑓: 0.29 ( 42018 hom. )

Consequence

LILRA6
ENST00000396365.7 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.628

Publications

15 publications found

Variant links:

Genes affected

LILRA6 (HGNC:15495): (leukocyte immunoglobulin like receptor A6) Predicted to enable inhibitory MHC class I receptor activity. Predicted to be involved in cytokine-mediated signaling pathway. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LILRA6 links:

RPS9 (HGNC:10442): (ribosomal protein S9) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S4P family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, multiple processed pseudogenes derived from this gene are dispersed through the genome. [provided by RefSeq, Jul 2008]

RPS9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002255261).

BP6

Variant 19-54241620-C-T is Benign according to our data. Variant chr19-54241620-C-T is described in ClinVar as Benign. ClinVar VariationId is 403040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRA6	NM_024318.5 link	c.614G>A	p.Arg205Gln	missense_variant	Exon 4 of 8		NP_077294.3	U5XH19
LILRA6	NR_104098.2 link	n.611+42G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRA6	ENST00000396365.7 link	c.614G>A	p.Arg205Gln	missense_variant	Exon 4 of 8	1		ENSP00000379651.2		Q6PI73

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

35130

AN:

115262

Hom.:

4175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.361

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.310

GnomAD2 exomes

AF:

0.0533

AC:

10421

AN:

195684

AF XY:

0.0508

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.0446

Gnomad ASJ exome

AF:

0.0259

Gnomad EAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.0607

Gnomad NFE exome

AF:

0.0380

Gnomad OTH exome

AF:

0.0564

GnomAD4 exome

AF:

0.290

AC:

330699

AN:

1139888

Hom.:

42018

Cov.:

AF XY:

0.295

AC XY:

168075

AN XY:

569790

show subpopulations

African (AFR)

AF:

0.315

AC:

8255

AN:

26168

American (AMR)

AF:

0.285

AC:

11106

AN:

39030

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

5090

AN:

20688

East Asian (EAS)

AF:

0.363

AC:

12796

AN:

35272

South Asian (SAS)

AF:

0.387

AC:

25653

AN:

66220

European-Finnish (FIN)

AF:

0.346

AC:

16209

AN:

46880

Middle Eastern (MID)

AF:

0.313

AC:

1337

AN:

4278

European-Non Finnish (NFE)

AF:

0.276

AC:

235569

AN:

853392

Other (OTH)

AF:

0.306

AC:

14684

AN:

47960

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

10730

21460

32189

42919

53649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7338

14676

22014

29352

36690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.305

AC:

35172

AN:

115360

Hom.:

4176

Cov.:

AF XY:

0.304

AC XY:

16927

AN XY:

55636

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.326

AC:

10428

AN:

32010

American (AMR)

AF:

0.317

AC:

3683

AN:

11636

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

542

AN:

2502

East Asian (EAS)

AF:

0.355

AC:

1493

AN:

4204

South Asian (SAS)

AF:

0.360

AC:

1062

AN:

2948

European-Finnish (FIN)

AF:

0.276

AC:

2118

AN:

7664

Middle Eastern (MID)

AF:

0.242

AC:

AN:

194

European-Non Finnish (NFE)

AF:

0.291

AC:

15108

AN:

51920

Other (OTH)

AF:

0.313

AC:

487

AN:

1558

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.378

Heterozygous variant carriers

1011

2022

3032

4043

5054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.202

Hom.:

577

ExAC

AF:

0.0352

AC:

4094

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.25

(source)

DANN

Benign

0.71

DEOGEN2

Benign

0.0021

.;T

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00019

LIST_S2

Benign

0.16

T;T

MetaRNN

Benign

0.0023

T;T

MetaSVM

Benign

-0.95

PhyloP100

-0.63

PROVEAN

Benign

1.4

N;N

REVEL

Benign

0.020

Sift

Benign

0.85

T;T

Sift4G

Benign

0.60

T;T

Vest4

0.029

MPC

1.1

ClinPred

0.000020

GERP RS

2.4

gMVP

0.095

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over