chr1-160827894-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002348.4(LY9):​c.*78A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002348.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY9	NM_002348.4	MANE Select	c.*78A>T		3_prime_UTR	Exon 10 of 10	NP_002339.2	Q9HBG7-1
	LY9	NM_001261456.2		c.*78A>T		3_prime_UTR	Exon 10 of 10	NP_001248385.1	Q9HBG7-2
	LY9	NM_001261457.2		c.*78A>T		3_prime_UTR	Exon 9 of 9	NP_001248386.1	Q5VYH9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY9	ENST00000263285.11	TSL:1 MANE Select	c.*78A>T		3_prime_UTR	Exon 10 of 10	ENSP00000263285.5	Q9HBG7-1
	LY9	ENST00000368037.10	TSL:1	c.*78A>T		3_prime_UTR	Exon 10 of 10	ENSP00000357016.5	Q9HBG7-2
	LY9	ENST00000392203.8	TSL:1	c.*78A>T		3_prime_UTR	Exon 9 of 9	ENSP00000376039.4	Q5VYH9

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 989026 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 506534

African (AFR) AF: 0.00 AC: 0 AN: 22578

American (AMR) AF: 0.00 AC: 0 AN: 32022

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19670

East Asian (EAS) AF: 0.00 AC: 0 AN: 35340

South Asian (SAS) AF: 0.00 AC: 0 AN: 66054

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4640

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 718330

Other (OTH) AF: 0.00 AC: 0 AN: 44126

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 8564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.48
PhyloP100		-2.4

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;