chr1-160827894-A-G

Position:

• chr1-160827894-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.*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

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=-0.97).
• 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/exons	MANE	Protein	UniProt
LY9	NM_002348.4	c.*78A>G		3_prime_UTR_variant	10/10	ENST00000263285.11	NP_002339.2

Ensembl

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

Gnomad4 AFR exome AF: 0.541

Gnomad4 AMR exome AF: 0.697

Gnomad4 ASJ exome AF: 0.551

Gnomad4 EAS exome AF: 0.744

Gnomad4 SAS exome AF: 0.619

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.456

Gnomad4 OTH exome AF: 0.514

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

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.540

Alfa AF: 0.485 Hom.: 7043

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

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

Other links and lift over

dbSNP: rs574610; hg19: chr1-160797684;