1-160823770-ATG-GTC

Variant names:

• chr1-160823770-ATG-GTC
• NM_002348.4:c.1804_1806delATGinsGTC
• LY9 p.Met602Val

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002348.4(LY9):​c.1804_1806delATGinsGTC​(p.Met602Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M602T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: LY9 NM_002348.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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.1804_1806delATGinsGTC	p.Met602Val	missense	N/A	NP_002339.2	Q9HBG7-1
	LY9	NM_001261456.2		c.1762_1764delATGinsGTC	p.Met588Val	missense	N/A	NP_001248385.1	Q9HBG7-2
	LY9	NM_001261457.2		c.1534_1536delATGinsGTC	p.Met512Val	missense	N/A	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.1804_1806delATGinsGTC	p.Met602Val	missense	N/A	ENSP00000263285.5	Q9HBG7-1
	LY9	ENST00000368037.10	TSL:1	c.1762_1764delATGinsGTC	p.Met588Val	missense	N/A	ENSP00000357016.5	Q9HBG7-2
	LY9	ENST00000392203.8	TSL:1	c.1534_1536delATGinsGTC	p.Met512Val	missense	N/A	ENSP00000376039.4	Q5VYH9

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-160793560;