Variant 1-160813767-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002348.4(LY9):c.586C>A(p.Pro196Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,614,140 control chromosomes in the GnomAD database, including 230 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0099 ( 13 hom., cov: 32)

Exomes 𝑓: 0.016 ( 217 hom. )

Consequence

LY9
NM_002348.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.70

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:

LY9 (HGNC:):

LY9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0028006732).

BP6

Variant 1-160813767-C-A is Benign according to our data. Variant chr1-160813767-C-A is described in ClinVar as [Benign]. Clinvar id is 783299.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0156 (22841/1461874) while in subpopulation NFE AF= 0.0185 (20626/1112000). AF 95% confidence interval is 0.0183. There are 217 homozygotes in gnomad4_exome. There are 10840 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LY9	NM_002348.4 linkuse as main transcript	c.586C>A	p.Pro196Thr	missense_variant	3/10	ENST00000263285.11	NP_002339.2	Q9HBG7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LY9	ENST00000263285.11 linkuse as main transcript	c.586C>A	p.Pro196Thr	missense_variant	3/10	1	NM_002348.4	ENSP00000263285.5		Q9HBG7-1

Frequencies

GnomAD3 genomes

AF:

0.00993

AC:

1511

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00309

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.00295

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.0214

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00935

AC:

2352

AN:

251454

Hom.:

AF XY:

0.00908

AC XY:

1234

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.00228

Gnomad AMR exome

AF:

0.00312

Gnomad ASJ exome

AF:

0.00407

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00225

Gnomad FIN exome

AF:

0.0181

Gnomad NFE exome

AF:

0.0146

Gnomad OTH exome

AF:

0.00831

GnomAD4 exome

AF:

0.0156

AC:

22841

AN:

1461874

Hom.:

217

Cov.:

AF XY:

0.0149

AC XY:

10840

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.00266

Gnomad4 AMR exome

AF:

0.00315

Gnomad4 ASJ exome

AF:

0.00539

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00221

Gnomad4 FIN exome

AF:

0.0184

Gnomad4 NFE exome

AF:

0.0185

Gnomad4 OTH exome

AF:

0.0107

GnomAD4 genome

AF:

0.00992

AC:

1510

AN:

152266

Hom.:

Cov.:

AF XY:

0.00971

AC XY:

723

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00308

Gnomad4 AMR

AF:

0.00294

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00270

Gnomad4 FIN

AF:

0.0214

Gnomad4 NFE

AF:

0.0150

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.0123

Hom.:

Bravo

AF:

0.00873

TwinsUK

AF:

0.0162

AC:

ALSPAC

AF:

0.0182

AC:

ESP6500AA

AF:

0.00409

AC:

ESP6500EA

AF:

0.0155

AC:

133

ExAC

AF:

0.00847

AC:

1029

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0152

EpiControl

AF:

0.0143

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 15, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.0010

DANN

Benign

0.23

DEOGEN2

Benign

0.16

.;.;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.3

FATHMM_MKL

Benign

0.0019

LIST_S2

Benign

0.55

T;T;T

MetaRNN

Benign

0.0028

T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.20

N;.;N

PrimateAI

Benign

0.20

PROVEAN

Benign

-2.0

.;.;N

REVEL

Benign

0.018

Sift

Benign

0.93

.;.;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0010

B;.;B

Vest4

0.078

MVP

0.14

MPC

0.072

ClinPred

0.012

GERP RS

-8.3

Varity_R

0.055

gMVP

0.30

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over