1-219173919-AG-CA

Variant names:

• chr1-219173919-AG-CA
• NM_138794.5:c.29_30delAGinsCA
• LYPLAL1 p.Gln10Pro

Variant summary

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

The NM_138794.5(LYPLAL1):​c.29_30delAGinsCA​(p.Gln10Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. The variant is present in control chromosomes in GnomAd MNV project. The variant allele was found at a frequency of 0.000004 in 1 alleles, including 0 homozygotes. 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 Uncertain significance in ClinVar.

• Frequency: GnomAD MNV: 𝑓 0.0000040 Genomes: not found (cov: 33)
• Consequence: LYPLAL1 NM_138794.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• Publications: 0 publications found

Genes affected

LYPLAL1 (HGNC:20440): (lysophospholipase like 1) Predicted to enable carboxylic ester hydrolase activity and palmitoyl-(protein) hydrolase activity. Predicted to be involved in protein depalmitoylation. Predicted to act upstream of or within negative regulation of Golgi to plasma membrane protein transport. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LYPLAL1-DT (HGNC:50560): (LYPLAL1 divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138794.5. 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
	LYPLAL1	NM_138794.5	MANE Select	c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	NP_620149.2	Q5VWZ2-1
	LYPLAL1	NM_001350628.2		c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	NP_001337557.1
	LYPLAL1	NM_001350629.2		c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	NP_001337558.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYPLAL1	ENST00000366928.10	TSL:1 MANE Select	c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	ENSP00000355895.5	Q5VWZ2-1
	LYPLAL1	ENST00000366927.3	TSL:1	c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	ENSP00000355894.3	Q5VWZ2-2
	LYPLAL1	ENST00000910159.1		c.29_30delAGinsCA	p.Gln10Pro	missense	N/A	ENSP00000580218.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

GnomAD MNV AF: 0.00000400 AC: 1 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

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: chr1-219347261;