Genetic Variant LY86:c.-9-78A>C (chr6-6588648-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000379953.6(LY86):c.-9-78A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 1,483,312 control chromosomes in the GnomAD database, including 392,704 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 0.71 ( 38176 hom., cov: 33)

Exomes 𝑓: 0.73 ( 354528 hom. )

Consequence

LY86
ENST00000379953.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

Publications

21 publications found

Variant links:

Genes affected

LY86 (HGNC:16837): (lymphocyte antigen 86) Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LY86 links:

LY86-AS1 (HGNC:26593): (LY86 antisense RNA 1)

LY86-AS1 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379953.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	NR_026970.1		n.196-19159T>G		intron	N/A
	LY86	NM_004271.4	MANE Select	c.-87A>C		upstream_gene	N/A	NP_004262.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LY86	ENST00000379953.6	TSL:5	c.-9-78A>C	intron	N/A	ENSP00000369286.1
LY86-AS1	ENST00000429345.5	TSL:2	n.114-19159T>G	intron	N/A
LY86-AS1	ENST00000435641.5	TSL:2	n.388+2508T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107659

AN:

152062

Hom.:

38163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.589

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.729

AC:

970839

AN:

1331132

Hom.:

354528

Cov.:

AF XY:

0.731

AC XY:

481575

AN XY:

658402

show subpopulations

African (AFR)

AF:

0.652

AC:

19640

AN:

30132

American (AMR)

AF:

0.731

AC:

27388

AN:

37484

Ashkenazi Jewish (ASJ)

AF:

0.775

AC:

17209

AN:

22192

East Asian (EAS)

AF:

0.672

AC:

25894

AN:

38560

South Asian (SAS)

AF:

0.749

AC:

55553

AN:

74190

European-Finnish (FIN)

AF:

0.741

AC:

34720

AN:

46834

Middle Eastern (MID)

AF:

0.772

AC:

3723

AN:

4820

European-Non Finnish (NFE)

AF:

0.730

AC:

746152

AN:

1021490

Other (OTH)

AF:

0.732

AC:

40560

AN:

55430

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

12282

24564

36847

49129

61411

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18570

37140

55710

74280

92850

<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:

0.708

AC:

107706

AN:

152180

Hom.:

38176

Cov.:

AF XY:

0.707

AC XY:

52576

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.651

AC:

26998

AN:

41488

American (AMR)

AF:

0.713

AC:

10902

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

2668

AN:

3472

East Asian (EAS)

AF:

0.660

AC:

3420

AN:

5184

South Asian (SAS)

AF:

0.739

AC:

3566

AN:

4826

European-Finnish (FIN)

AF:

0.751

AC:

7950

AN:

10590

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.735

AC:

49975

AN:

68008

Other (OTH)

AF:

0.697

AC:

1474

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1662

3325

4987

6650

8312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.727

Hom.:

128177

Bravo

AF:

0.704

Asia WGS

AF:

0.655

AC:

2278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.5

(source)

DANN

Benign

0.74

PhyloP100

0.068

PromoterAI

-0.18

Neutral

(source)

Mutation Taster

=100/0

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