dbSNP rs2287828: LAIR2:c.-11G>A (chr19-54502908-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002288.6(LAIR2):c.-11G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,613,794 control chromosomes in the GnomAD database, including 5,075 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.056 ( 651 hom., cov: 31)

Exomes 𝑓: 0.047 ( 4424 hom. )

Consequence

LAIR2
NM_002288.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.136

Publications

11 publications found

Variant links:

Genes affected

LAIR2 (HGNC:6478): (leukocyte associated immunoglobulin like receptor 2) The protein encoded by this gene is a member of the immunoglobulin superfamily. It was identified by its similarity to leukocyte-associated immunoglobulin-like receptor 1, a membrane-bound receptor that modulates innate immune response. The protein encoded by this locus is a soluble receptor that may play roles in both inhibition of collagen-induced platelet aggregation and vessel formation during placental implantation. This gene maps to a region of 19q13.4, termed the leukocyte receptor cluster, which contains 29 genes in the immunoglobulin superfamily. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2013]

LAIR2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002288.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAIR2	NM_002288.6	MANE Select	c.-11G>A		5_prime_UTR	Exon 1 of 5	NP_002279.2
	LAIR2	NM_021270.5		c.-11G>A		5_prime_UTR	Exon 1 of 4	NP_067154.1	Q6ISS4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LAIR2	ENST00000301202.7	TSL:1 MANE Select	c.-11G>A	5_prime_UTR	Exon 1 of 5	ENSP00000301202.2	Q6ISS4-1
LAIR2	ENST00000351841.2	TSL:1	c.-11G>A	5_prime_UTR	Exon 1 of 4	ENSP00000301203.2	Q6ISS4-2
LAIR2	ENST00000412608.5	TSL:1	c.17-792G>A	intron	N/A	ENSP00000390729.1	C9JFQ0

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8416

AN:

152060

Hom.:

637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0242

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.0788

Gnomad FIN

AF:

0.0691

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.0271

Gnomad OTH

AF:

0.0632

GnomAD2 exomes

AF:

0.0903

AC:

22693

AN:

251226

AF XY:

0.0800

show subpopulations

Gnomad AFR exome

AF:

0.0236

Gnomad AMR exome

AF:

0.286

Gnomad ASJ exome

AF:

0.0182

Gnomad EAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.0691

Gnomad NFE exome

AF:

0.0263

Gnomad OTH exome

AF:

0.0659

GnomAD4 exome

AF:

0.0470

AC:

68725

AN:

1461616

Hom.:

4424

Cov.:

AF XY:

0.0460

AC XY:

33453

AN XY:

727124

show subpopulations

African (AFR)

AF:

0.0226

AC:

758

AN:

33468

American (AMR)

AF:

0.280

AC:

12509

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.0212

AC:

555

AN:

26132

East Asian (EAS)

AF:

0.263

AC:

10453

AN:

39688

South Asian (SAS)

AF:

0.0621

AC:

5357

AN:

86252

European-Finnish (FIN)

AF:

0.0697

AC:

3725

AN:

53416

Middle Eastern (MID)

AF:

0.0187

AC:

108

AN:

5768

European-Non Finnish (NFE)

AF:

0.0288

AC:

31985

AN:

1111808

Other (OTH)

AF:

0.0542

AC:

3275

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

2885

5771

8656

11542

14427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1556

3112

4668

6224

7780

<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:

0.0555

AC:

8448

AN:

152178

Hom.:

651

Cov.:

AF XY:

0.0608

AC XY:

4527

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0243

AC:

1010

AN:

41538

American (AMR)

AF:

0.181

AC:

2766

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0193

AC:

AN:

3470

East Asian (EAS)

AF:

0.288

AC:

1489

AN:

5164

South Asian (SAS)

AF:

0.0785

AC:

379

AN:

4830

European-Finnish (FIN)

AF:

0.0691

AC:

732

AN:

10594

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0271

AC:

1841

AN:

67978

Other (OTH)

AF:

0.0640

AC:

135

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

358

716

1075

1433

1791

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0472

Hom.:

867

Bravo

AF:

0.0664

Asia WGS

AF:

0.170

AC:

590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.5

(source)

DANN

Benign

0.56

PhyloP100

-0.14

PromoterAI

0.020

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over