chr1-219519878-G-A

Variant names:

• chr1-219519878-G-A
• rs2820464
• ENST00000811290.1:n.60+29972C>T

Variant summary

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

The ENST00000811290.1(LYPLAL1-AS1):​n.60+29972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,938 control chromosomes in the GnomAD database, including 6,686 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 0.28 (6686 hom., cov: 32)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 21 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.134+37313C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000811290.1	n.60+29972C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42549 AN: 151820 Hom.: 6680 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.280 AC: 42574 AN: 151938 Hom.: 6686 Cov.: 32 AF XY: 0.284 AC XY: 21064 AN XY: 74252

African (AFR) AF: 0.147 AC: 6071 AN: 41432

American (AMR) AF: 0.419 AC: 6396 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 899 AN: 3464

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5158

South Asian (SAS) AF: 0.252 AC: 1215 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3561 AN: 10534

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22209 AN: 67944

Other (OTH) AF: 0.292 AC: 615 AN: 2106

Alfa AF: 0.299 Hom.: 12075

Bravo AF: 0.284

Asia WGS AF: 0.259 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2820464; hg19: chr1-219693220; COSMIC: COSV60029315;