Genetic Variant NM_002346.3: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY6E	NM_002346.3 link	c.52+85C>T		intron_variant	Intron 2 of 3	ENST00000292494.11	NP_002337.1
LY6E	NM_001127213.2 link	c.52+85C>T		intron_variant	Intron 2 of 3		NP_001120685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY6E	ENST00000292494.11 link	c.52+85C>T		intron_variant	Intron 2 of 3	1	NM_002346.3	ENSP00000292494.6		Q16553

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over