dbSNP rs11136286: LY6E:c.52+85C>T (chr8-143021076-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR exome

AF:

0.237

Gnomad4 AMR exome

AF:

0.368

Gnomad4 ASJ exome

AF:

0.277

Gnomad4 EAS exome

AF:

0.562

Gnomad4 SAS exome

AF:

0.232

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.319

AC:

48545

AN:

151986

Hom.:

8263

Cov.:

AF XY:

0.320

AC XY:

23793

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.377

Gnomad4 ASJ

AF:

0.282

Gnomad4 EAS

AF:

0.557

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.399

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.322

Alfa

AF:

0.312

Hom.:

2032

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

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over