chr1-219431111-C-T

Variant names:

• chr1-219431111-C-T
• rs17005517
• ENST00000441790.2:n.121-19172G>A

Variant summary

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

The ENST00000441790.2(LYPLAL1-AS1):​n.121-19172G>A variant causes a intron 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: 32)
• Consequence: LYPLAL1-AS1 ENST00000441790.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 5 publications found

Genes affected

LYPLAL1-AS1 (HGNC:54054): (LYPLAL1 antisense RNA 1)

ENSG00000305547 (HGNC:):

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]

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1	XR_001736967.3	n.1057-949C>T		intron_variant	Intron 7 of 9
LOC107984018	XR_002958459.2	n.146+1792G>A		intron_variant	Intron 1 of 3
LOC107984018	XR_002958460.2	n.146+1792G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000441790.2	n.121-19172G>A		intron_variant	Intron 1 of 2	5
LYPLAL1-AS1	ENST00000652910.1	n.179+1792G>A		intron_variant	Intron 1 of 4
LYPLAL1-AS1	ENST00000653604.1	n.240+1792G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.46
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs17005517; hg19: chr1-219604453;