rs2605100

chr1-219470882-A-G

Variant summary

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

The NR_135822.1(LYPLAL1-AS1):n.135-1039T>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 0.765 in 152,098 control chromosomes in the GnomAD database, including 45,039 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 0.76 (45039 hom., cov: 31)
• Consequence: LYPLAL1-AS1 NR_135822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

LYPLAL1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYPLAL1-AS1	NR_135822.1	n.135-1039T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116176 AN: 151980 Hom.: 44987 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.765 AC: 116288 AN: 152098 Hom.: 45039 Cov.: 31 AF XY: 0.763 AC XY: 56742 AN XY: 74346

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.764

Alfa AF: 0.723 Hom.: 88251

Bravo AF: 0.768

Asia WGS AF: 0.836 AC: 2909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.063
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2605100; hg19: chr1-219644224;