rs4846565

Variant names:

• chr1-219548762-G-A
• rs4846565
• ENST00000811290.1:n.60+1088C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-219548762-G-A
• chr1-219548762-G-C

Variant summary

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

The ENST00000811290.1(LYPLAL1-AS1):​n.60+1088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,042 control chromosomes in the GnomAD database, including 6,350 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 0.26 (6350 hom., cov: 32)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 35 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.134+8429C>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.60+1088C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40000 AN: 151924 Hom.: 6346 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.263 AC: 40015 AN: 152042 Hom.: 6350 Cov.: 32 AF XY: 0.267 AC XY: 19836 AN XY: 74320

African (AFR) AF: 0.0840 AC: 3488 AN: 41508

American (AMR) AF: 0.410 AC: 6260 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1337 AN: 5156

South Asian (SAS) AF: 0.251 AC: 1206 AN: 4814

European-Finnish (FIN) AF: 0.352 AC: 3711 AN: 10556

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22337 AN: 67946

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.285 Hom.: 4665

Bravo AF: 0.263

Asia WGS AF: 0.251 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs4846565; hg19: chr1-219722104;