rs12022722

Variant names:

• chr1-219477791-C-T
• rs12022722
• ENST00000811290.1:n.61-7951G>A

Variant summary

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

The ENST00000811290.1(LYPLAL1-AS1):​n.61-7951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,100 control chromosomes in the GnomAD database, including 11,356 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 (11356 hom., cov: 33)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• 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=-0.71).
• 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.135-7948G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000811290.1	n.61-7951G>A		intron_variant	Intron 1 of 2
LYPLAL1-AS1	ENST00000811291.1	n.120-7948G>A		intron_variant	Intron 1 of 3
LYPLAL1-AS1	ENST00000811292.1	n.98-7948G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52747 AN: 151982 Hom.: 11360 Cov.: 33

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.347 AC: 52743 AN: 152100 Hom.: 11356 Cov.: 33 AF XY: 0.347 AC XY: 25792 AN XY: 74340

African (AFR) AF: 0.0912 AC: 3787 AN: 41524

American (AMR) AF: 0.332 AC: 5079 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5184

South Asian (SAS) AF: 0.483 AC: 2333 AN: 4826

European-Finnish (FIN) AF: 0.470 AC: 4953 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31822 AN: 67960

Other (OTH) AF: 0.397 AC: 836 AN: 2108

Alfa AF: 0.431 Hom.: 51074

Bravo AF: 0.321

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12022722; hg19: chr1-219651133;