ENST00000441790.2:n.121-3522T>C

Variant names:

• chr1-219415461-A-G
• rs2791559
• ENST00000441790.2:n.121-3522T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441790.2(LYPLAL1-AS1):​n.121-3522T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,130 control chromosomes in the GnomAD database, including 13,650 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 0.41 (13650 hom., cov: 33)
• Consequence: LYPLAL1-AS1 ENST00000441790.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 11 publications found

Genes affected

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

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]

LOC107984018 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1	XR_001736967.3	n.1057-16599A>G		intron_variant	Intron 7 of 9
LOC107984018	XR_002958458.2	n.453-3522T>C		intron_variant	Intron 2 of 3
LOC107984018	XR_002958459.2	n.199-3522T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000441790.2	n.121-3522T>C		intron_variant	Intron 1 of 2	5
LYPLAL1-AS1	ENST00000652910.1	n.363-3522T>C		intron_variant	Intron 3 of 4
LYPLAL1-AS1	ENST00000653604.1	n.424-3522T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61839 AN: 152012 Hom.: 13636 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.407 AC: 61881 AN: 152130 Hom.: 13650 Cov.: 33 AF XY: 0.409 AC XY: 30441 AN XY: 74384

African (AFR) AF: 0.268 AC: 11109 AN: 41512

American (AMR) AF: 0.550 AC: 8404 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4140 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2134 AN: 4828

European-Finnish (FIN) AF: 0.381 AC: 4036 AN: 10582

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29545 AN: 67980

Other (OTH) AF: 0.400 AC: 844 AN: 2112

Alfa AF: 0.428 Hom.: 25868

Bravo AF: 0.418

Asia WGS AF: 0.588 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2791559; hg19: chr1-219588803;