NR_135822.1:n.134+2754A>G

Variant names:

• chr1-219554437-T-C
• rs3001032
• NR_135822.1:n.134+2754A>G

Variant summary

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

The NR_135822.1(LYPLAL1-AS1):​n.134+2754A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,864 control chromosomes in the GnomAD database, including 9,858 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 0.35 (9858 hom., cov: 32)
• Consequence: LYPLAL1-AS1 NR_135822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 31 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_135822.1. 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
	LYPLAL1-AS1	NR_135822.1		n.134+2754A>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53470 AN: 151746 Hom.: 9844 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53537 AN: 151864 Hom.: 9858 Cov.: 32 AF XY: 0.353 AC XY: 26233 AN XY: 74242

African (AFR) AF: 0.439 AC: 18187 AN: 41386

American (AMR) AF: 0.453 AC: 6910 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1392 AN: 5148

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3363 AN: 10552

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20524 AN: 67942

Other (OTH) AF: 0.350 AC: 738 AN: 2106

Alfa AF: 0.318 Hom.: 32107

Bravo AF: 0.371

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.45
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3001032; hg19: chr1-219727779; COSMIC: COSV71729967;