rs2605100

Variant names:

• chr1-219470882-A-G
• rs2605100
• ENST00000811293.1:n.67T>C

Variant summary

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

The ENST00000811293.1(LYPLAL1-AS1):​n.67T>C variant causes a non coding transcript exon 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 ENST00000811293.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 76 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=-0.9).
• 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 rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.135-1039T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000811293.1	n.67T>C		non_coding_transcript_exon_variant	Exon 1 of 4
LYPLAL1-AS1	ENST00000811295.1	n.23T>C		non_coding_transcript_exon_variant	Exon 1 of 5
LYPLAL1-AS1	ENST00000811290.1	n.61-1042T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.891 AC: 36996 AN: 41528

American (AMR) AF: 0.695 AC: 10610 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2638 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4326 AN: 5172

South Asian (SAS) AF: 0.820 AC: 3943 AN: 4808

European-Finnish (FIN) AF: 0.673 AC: 7112 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 48006 AN: 67970

Other (OTH) AF: 0.764 AC: 1614 AN: 2112

Alfa AF: 0.727 Hom.: 172424

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2605100; hg19: chr1-219644224;