rs2791559

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441790.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYPLAL1-AS1	ENST00000441790.2	TSL:5	n.121-3522T>C		intron	N/A
	LYPLAL1-AS1	ENST00000652910.1		n.363-3522T>C		intron	N/A
	LYPLAL1-AS1	ENST00000653604.1		n.424-3522T>C		intron	N/A

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 v4.9

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;