1-219502700-A-G

Variant names:

• chr1-219502700-A-G
• rs2791553
• ENST00000811290.1:n.61-32860T>C

Variant summary

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

The ENST00000811290.1(LYPLAL1-AS1):​n.61-32860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,986 control chromosomes in the GnomAD database, including 24,764 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 0.57 (24764 hom., cov: 32)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 16 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.135-32857T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000811290.1	n.61-32860T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85841 AN: 151868 Hom.: 24753 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.565 AC: 85885 AN: 151986 Hom.: 24764 Cov.: 32 AF XY: 0.562 AC XY: 41738 AN XY: 74288

African (AFR) AF: 0.546 AC: 22611 AN: 41450

American (AMR) AF: 0.427 AC: 6522 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2237 AN: 3460

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5168

South Asian (SAS) AF: 0.658 AC: 3171 AN: 4816

European-Finnish (FIN) AF: 0.612 AC: 6456 AN: 10546

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41205 AN: 67966

Other (OTH) AF: 0.566 AC: 1194 AN: 2108

Alfa AF: 0.587 Hom.: 53880

Bravo AF: 0.542

Asia WGS AF: 0.536 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.069
DANN	Benign	0.75
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2791553; hg19: chr1-219676042;