Genetic Variant LY9:c.*520A>G (chr1-160828336-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 ENST00000368037.10(LY9):c.*520A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,988 control chromosomes in the GnomAD database, including 17,831 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 0.48 ( 17822 hom., cov: 32)

Exomes 𝑓: 0.43 ( 9 hom. )

Consequence

LY9
ENST00000368037.10 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.825

Publications

6 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

new If you want to explore the variant's impact on the transcript ENST00000368037.10, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368037.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LY9	NM_002348.4	MANE Select	c.*520A>G	downstream_gene	N/A	NP_002339.2	Q9HBG7-1
LY9	NM_001261456.2		c.*520A>G	downstream_gene	N/A	NP_001248385.1	Q9HBG7-2
LY9	NM_001261457.2		c.*520A>G	downstream_gene	N/A	NP_001248386.1	Q5VYH9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LY9	ENST00000368037.10	TSL:1	c.*520A>G	3_prime_UTR	Exon 10 of 10	ENSP00000357016.5	Q9HBG7-2
LY9	ENST00000263285.11	TSL:1 MANE Select	c.*520A>G	downstream_gene	N/A	ENSP00000263285.5	Q9HBG7-1
LY9	ENST00000392203.8	TSL:1	c.*520A>G	downstream_gene	N/A	ENSP00000376039.4	Q5VYH9

Frequencies

GnomAD3 genomes

AF:

0.480

AC:

72818

AN:

151812

Hom.:

17798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.589

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.707

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.449

Gnomad OTH

AF:

0.518

GnomAD4 exome

AF:

0.431

AC:

AN:

Hom.:

AF XY:

0.433

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.389

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.480

AC:

72894

AN:

151930

Hom.:

17822

Cov.:

AF XY:

0.485

AC XY:

35990

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.442

AC:

18302

AN:

41408

American (AMR)

AF:

0.590

AC:

9006

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

1879

AN:

3468

East Asian (EAS)

AF:

0.708

AC:

3654

AN:

5164

South Asian (SAS)

AF:

0.623

AC:

2999

AN:

4810

European-Finnish (FIN)

AF:

0.482

AC:

5083

AN:

10546

Middle Eastern (MID)

AF:

0.459

AC:

133

AN:

290

European-Non Finnish (NFE)

AF:

0.449

AC:

30539

AN:

67956

Other (OTH)

AF:

0.519

AC:

1094

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1903

3805

5708

7610

9513

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.479

Hom.:

5795

Bravo

AF:

0.486

Asia WGS

AF:

0.689

AC:

2396

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.4

(source)

DANN

Benign

0.61

PhyloP100

0.82

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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