rs12022722

Positions:

• chr1-219477791-C-T

Variant summary

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

The NR_135822.1(LYPLAL1-AS1):​n.135-7948G>A 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 0.347 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 NR_135822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

LYPLAL1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.135-7948G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0912

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.397

Alfa AF: 0.460 Hom.: 33192

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12022722; hg19: chr1-219651133;