Genetic Variant LY6E:c.52+85C>T (chr8-143021076-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002346.3(LY6E):c.52+85C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,473,594 control chromosomes in the GnomAD database, including 81,957 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 0.32 ( 8263 hom., cov: 32)

Exomes 𝑓: 0.33 ( 73694 hom. )

Consequence

LY6E
NM_002346.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

7 publications found

Variant links:

Genes affected

LY6E (HGNC:6727): (lymphocyte antigen 6 family member E) This gene belongs to the human Ly6 gene family and encodes a glycosylphosphatidyl-inositol (GPI)-anchored cell surface protein. The protein plays an important role in T cell physiology, oncogenesis and immunological regulation. The protein is also involved in modulation of viral infection by coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2. [provided by RefSeq, Aug 2021]

LY6E 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002346.3. 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
	LY6E	NM_002346.3	MANE Select	c.52+85C>T		intron	N/A	NP_002337.1	Q16553
	LY6E	NM_001127213.2		c.52+85C>T		intron	N/A	NP_001120685.1	Q16553

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LY6E	ENST00000292494.11	TSL:1 MANE Select	c.52+85C>T	intron	N/A	ENSP00000292494.6	Q16553
LY6E	ENST00000429120.6	TSL:1	c.52+85C>T	intron	N/A	ENSP00000414307.2	Q16553
LY6E	ENST00000521182.5	TSL:1	c.52+85C>T	intron	N/A	ENSP00000430770.1	E5RI58

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48514

AN:

151868

Hom.:

8249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.556

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.316

GnomAD4 exome

AF:

0.329

AC:

434529

AN:

1321608

Hom.:

73694

AF XY:

0.326

AC XY:

215279

AN XY:

660540

show subpopulations

African (AFR)

AF:

0.237

AC:

7277

AN:

30764

American (AMR)

AF:

0.368

AC:

15109

AN:

41108

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

6466

AN:

23324

East Asian (EAS)

AF:

0.562

AC:

21586

AN:

38428

South Asian (SAS)

AF:

0.232

AC:

18375

AN:

79276

European-Finnish (FIN)

AF:

0.390

AC:

19192

AN:

49264

Middle Eastern (MID)

AF:

0.291

AC:

1553

AN:

5336

European-Non Finnish (NFE)

AF:

0.327

AC:

326767

AN:

998612

Other (OTH)

AF:

0.328

AC:

18204

AN:

55496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

14772

29543

44315

59086

73858

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10292

20584

30876

41168

51460

<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:

0.319

AC:

48545

AN:

151986

Hom.:

8263

Cov.:

AF XY:

0.320

AC XY:

23793

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.245

AC:

10182

AN:

41494

American (AMR)

AF:

0.377

AC:

5754

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.282

AC:

977

AN:

3470

East Asian (EAS)

AF:

0.557

AC:

2861

AN:

5140

South Asian (SAS)

AF:

0.230

AC:

1107

AN:

4820

European-Finnish (FIN)

AF:

0.399

AC:

4222

AN:

10574

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.330

AC:

22403

AN:

67900

Other (OTH)

AF:

0.322

AC:

679

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1641

3282

4924

6565

8206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.314

Hom.:

2335

Bravo

AF:

0.318

Asia WGS

AF:

0.374

AC:

1299

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

1.9

(source)

DANN

Benign

0.66

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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