rs2791559

Positions:

• chr1-219415461-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441790.2(LYPLAL1-AS1):​n.121-3522T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

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

LOC107984018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984018	XR_002958460.2	n.147-3522T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYPLAL1-AS1	ENST00000441790.2	n.121-3522T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.400

Alfa AF: 0.430 Hom.: 19535

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2791559; hg19: chr1-219588803;