chr1-219431111-C-A

Variant names:

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

Variant summary

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

The ENST00000441790.2(LYPLAL1-AS1):​n.121-19172G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,040 control chromosomes in the GnomAD database, including 5,053 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 0.25 (5053 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1	XR_001736967.3	n.1057-949C>A		intron_variant	Intron 7 of 9
LOC107984018	XR_002958459.2	n.146+1792G>T		intron_variant	Intron 1 of 3
LOC107984018	XR_002958460.2	n.146+1792G>T		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>T		intron_variant	Intron 1 of 2	5
LYPLAL1-AS1	ENST00000652910.1	n.179+1792G>T		intron_variant	Intron 1 of 4
LYPLAL1-AS1	ENST00000653604.1	n.240+1792G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38699 AN: 151922 Hom.: 5051 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.255 AC: 38712 AN: 152040 Hom.: 5053 Cov.: 32 AF XY: 0.249 AC XY: 18530 AN XY: 74328

African (AFR) AF: 0.256 AC: 10605 AN: 41454

American (AMR) AF: 0.197 AC: 3009 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1217 AN: 5144

South Asian (SAS) AF: 0.159 AC: 767 AN: 4812

European-Finnish (FIN) AF: 0.223 AC: 2352 AN: 10566

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18778 AN: 67984

Other (OTH) AF: 0.261 AC: 552 AN: 2116

Alfa AF: 0.268 Hom.: 15838

Bravo AF: 0.255

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.40
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;