1-160827894-A-G

Variant names:

• chr1-160827894-A-G
• rs574610
• NM_002348.4:c.*78A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002348.4(LY9):​c.*78A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,138,274 control chromosomes in the GnomAD database, including 143,863 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 0.51 (19858 hom., cov: 30)
  • Exomes 𝑓: 0.49 (124005 hom.)
• Consequence: LY9 NM_002348.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY9	NM_002348.4	c.*78A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000263285.11	NP_002339.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY9	ENST00000263285.11	c.*78A>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_002348.4	ENSP00000263285.5
LY9	ENST00000368037.10	c.*78A>G		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000357016.5
LY9	ENST00000392203.8	c.*78A>G		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000376039.4
LY9	ENST00000368035.1	c.*78A>G		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000357014.2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76965 AN: 151750 Hom.: 19828 Cov.: 30

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.493 AC: 486748 AN: 986406 Hom.: 124005 Cov.: 12 AF XY: 0.496 AC XY: 250535 AN XY: 505250

African (AFR) AF: 0.541 AC: 12190 AN: 22528

American (AMR) AF: 0.697 AC: 22268 AN: 31970

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 10806 AN: 19610

East Asian (EAS) AF: 0.744 AC: 26255 AN: 35266

South Asian (SAS) AF: 0.619 AC: 40832 AN: 65928

European-Finnish (FIN) AF: 0.499 AC: 23017 AN: 46128

Middle Eastern (MID) AF: 0.516 AC: 2385 AN: 4624

European-Non Finnish (NFE) AF: 0.456 AC: 326357 AN: 716314

Other (OTH) AF: 0.514 AC: 22638 AN: 44038

GnomAD4 genome AF: 0.507 AC: 77051 AN: 151868 Hom.: 19858 Cov.: 30 AF XY: 0.512 AC XY: 38001 AN XY: 74246

African (AFR) AF: 0.535 AC: 22128 AN: 41366

American (AMR) AF: 0.601 AC: 9176 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3636 AN: 5160

South Asian (SAS) AF: 0.632 AC: 3041 AN: 4810

European-Finnish (FIN) AF: 0.483 AC: 5090 AN: 10548

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30618 AN: 67928

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.487 Hom.: 8564

Bravo AF: 0.516

Asia WGS AF: 0.700 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.073
DANN	Benign	0.42
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs574610; hg19: chr1-160797684;