rs11118316

Variant names:

• chr1-219483821-G-A
• rs11118316
• ENST00000811290.1:n.61-13981C>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.61-13981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,806 control chromosomes in the GnomAD database, including 11,429 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 (11429 hom., cov: 33)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 22 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.135-13978C>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.61-13981C>T		intron_variant	Intron 1 of 2
LYPLAL1-AS1	ENST00000811291.1	n.119+11982C>T		intron_variant	Intron 1 of 3
LYPLAL1-AS1	ENST00000811292.1	n.97+11982C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52875 AN: 151688 Hom.: 11431 Cov.: 33

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.348 AC: 52873 AN: 151806 Hom.: 11429 Cov.: 33 AF XY: 0.349 AC XY: 25857 AN XY: 74184

African (AFR) AF: 0.0918 AC: 3810 AN: 41498

American (AMR) AF: 0.338 AC: 5164 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1705 AN: 3464

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5164

South Asian (SAS) AF: 0.483 AC: 2329 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4957 AN: 10532

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31884 AN: 67740

Other (OTH) AF: 0.402 AC: 844 AN: 2102

Alfa AF: 0.435 Hom.: 41250

Bravo AF: 0.323

Asia WGS AF: 0.406 AC: 1411 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11118316; hg19: chr1-219657163;