rs560681

Positions:

• chr1-160816880-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002348.4(LY9):​c.1342+17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,612,806 control chromosomes in the GnomAD database, including 79,426 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 0.31 (7471 hom., cov: 31)
  • Exomes 𝑓: 0.31 (71955 hom.)
• Consequence: LY9 NM_002348.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LY9	NM_002348.4	c.1342+17A>G		intron_variant		ENST00000263285.11	NP_002339.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LY9	ENST00000263285.11	c.1342+17A>G		intron_variant		1	NM_002348.4	ENSP00000263285	P2
LY9	ENST00000368035.1	c.509+17A>G		intron_variant		1		ENSP00000357014
LY9	ENST00000368037.9	c.1342+17A>G		intron_variant		1		ENSP00000357016	A2
LY9	ENST00000392203.8	c.1073-1338A>G		intron_variant		1		ENSP00000376039

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47291 AN: 151808 Hom.: 7468 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.308

GnomAD3 exomes AF: 0.317 AC: 79558 AN: 250666 Hom.: 12938 AF XY: 0.325 AC XY: 44072 AN XY: 135536

Gnomad AFR exome AF: 0.312

Gnomad AMR exome AF: 0.266

Gnomad ASJ exome AF: 0.348

Gnomad EAS exome AF: 0.361

Gnomad SAS exome AF: 0.422

Gnomad FIN exome AF: 0.269

Gnomad NFE exome AF: 0.305

Gnomad OTH exome AF: 0.319

GnomAD4 exome AF: 0.310 AC: 453187 AN: 1460880 Hom.: 71955 Cov.: 34 AF XY: 0.314 AC XY: 228121 AN XY: 726768

Gnomad4 AFR exome AF: 0.311

Gnomad4 AMR exome AF: 0.270

Gnomad4 ASJ exome AF: 0.346

Gnomad4 EAS exome AF: 0.385

Gnomad4 SAS exome AF: 0.425

Gnomad4 FIN exome AF: 0.275

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.328

GnomAD4 genome AF: 0.311 AC: 47313 AN: 151926 Hom.: 7471 Cov.: 31 AF XY: 0.312 AC XY: 23157 AN XY: 74252

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.310

Alfa AF: 0.306 Hom.: 12653

Bravo AF: 0.308

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs560681; hg19: chr1-160786670; COSMIC: COSV54432438; COSMIC: COSV54432438;