Genetic Variant LY9:c.1342+17A>G (chr1-160816880-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002348.4(LY9):c.1342+17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,612,806 control chromosomes in the GnomAD database, including 79,426 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 0.31 ( 7471 hom., cov: 31)

Exomes 𝑓: 0.31 ( 71955 hom. )

Consequence

LY9
NM_002348.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.391

Publications

28 publications found

Variant links:

Genes affected

LY9 (HGNC:6730): (lymphocyte antigen 9) LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]

LY9 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY9	NM_002348.4 link	c.1342+17A>G		intron_variant	Intron 5 of 9	ENST00000263285.11	NP_002339.2	Q9HBG7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LY9	ENST00000263285.11 link	c.1342+17A>G	intron_variant	Intron 5 of 9	1	NM_002348.4	ENSP00000263285.5	Q9HBG7-1
LY9	ENST00000368037.10 link	c.1342+17A>G	intron_variant	Intron 5 of 9	1		ENSP00000357016.5	Q9HBG7-2
LY9	ENST00000392203.8 link	c.1073-1338A>G	intron_variant	Intron 4 of 8	1		ENSP00000376039.4	Q5VYH9
LY9	ENST00000368035.1 link	c.508+17A>G	intron_variant	Intron 2 of 5	1		ENSP00000357014.2	Q5VYI1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47291

AN:

151808

Hom.:

7468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.308

GnomAD2 exomes

AF:

0.317

AC:

79558

AN:

250666

AF XY:

0.325

show subpopulations

Gnomad AFR exome

AF:

0.312

Gnomad AMR exome

AF:

0.266

Gnomad ASJ exome

AF:

0.348

Gnomad EAS exome

AF:

0.361

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.305

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.310

AC:

453187

AN:

1460880

Hom.:

71955

Cov.:

AF XY:

0.314

AC XY:

228121

AN XY:

726768

show subpopulations

African (AFR)

AF:

0.311

AC:

10405

AN:

33454

American (AMR)

AF:

0.270

AC:

12091

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

9035

AN:

26120

East Asian (EAS)

AF:

0.385

AC:

15276

AN:

39666

South Asian (SAS)

AF:

0.425

AC:

36664

AN:

86224

European-Finnish (FIN)

AF:

0.275

AC:

14685

AN:

53392

Middle Eastern (MID)

AF:

0.378

AC:

2179

AN:

5766

European-Non Finnish (NFE)

AF:

0.300

AC:

333068

AN:

1111176

Other (OTH)

AF:

0.328

AC:

19784

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

16088

32176

48263

64351

80439

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11072

22144

33216

44288

55360

<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:

0.311

AC:

47313

AN:

151926

Hom.:

7471

Cov.:

AF XY:

0.312

AC XY:

23157

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.318

AC:

13172

AN:

41420

American (AMR)

AF:

0.296

AC:

4519

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1180

AN:

3468

East Asian (EAS)

AF:

0.370

AC:

1907

AN:

5156

South Asian (SAS)

AF:

0.416

AC:

2003

AN:

4816

European-Finnish (FIN)

AF:

0.266

AC:

2800

AN:

10534

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.305

AC:

20742

AN:

67946

Other (OTH)

AF:

0.310

AC:

654

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1676

3352

5027

6703

8379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.306

Hom.:

28433

Bravo

AF:

0.308

Asia WGS

AF:

0.387

AC:

1349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.5

(source)

DANN

Benign

0.60

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over