chr1-160828336-A-G

Variant names:

• chr1-160828336-A-G
• rs512645
• ENST00000368037.10:c.*520A>G

Variant summary

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

The ENST00000368037.10(LY9):​c.*520A>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 0.48 in 151,988 control chromosomes in the GnomAD database, including 17,831 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 0.48 (17822 hom., cov: 32)
  • Exomes 𝑓: 0.43 (9 hom.)
• Consequence: LY9 ENST00000368037.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368037.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY9	NM_002348.4	MANE Select	c.*520A>G		downstream_gene	N/A	NP_002339.2
	LY9	NM_001261456.2		c.*520A>G		downstream_gene	N/A	NP_001248385.1
	LY9	NM_001261457.2		c.*520A>G		downstream_gene	N/A	NP_001248386.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY9	ENST00000368037.10	TSL:1	c.*520A>G		3_prime_UTR	Exon 10 of 10	ENSP00000357016.5
	LY9	ENST00000263285.11	TSL:1 MANE Select	c.*520A>G		downstream_gene	N/A	ENSP00000263285.5
	LY9	ENST00000392203.8	TSL:1	c.*520A>G		downstream_gene	N/A	ENSP00000376039.4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72818 AN: 151812 Hom.: 17798 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.518

GnomAD4 exome AF: 0.431 AC: 25 AN: 58 Hom.: 9 AF XY: 0.433 AC XY: 13 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.389 AC: 21 AN: 54

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.480 AC: 72894 AN: 151930 Hom.: 17822 Cov.: 32 AF XY: 0.485 AC XY: 35990 AN XY: 74222

African (AFR) AF: 0.442 AC: 18302 AN: 41408

American (AMR) AF: 0.590 AC: 9006 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1879 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3654 AN: 5164

South Asian (SAS) AF: 0.623 AC: 2999 AN: 4810

European-Finnish (FIN) AF: 0.482 AC: 5083 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.449 AC: 30539 AN: 67956

Other (OTH) AF: 0.519 AC: 1094 AN: 2108

Alfa AF: 0.479 Hom.: 5795

Bravo AF: 0.486

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.61
PhyloP100		0.82
Mutation Taster		=98/2	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs512645; hg19: chr1-160798126;