rs84486

Variant names:

• chr22-25402889-G-A
• rs84486
• ENST00000444995.7:n.176+2313C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-25402889-G-A
• chr22-25402889-G-C
• chr22-25402889-G-T

Variant summary

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

The ENST00000444995.7(ENSG00000290796):​n.176+2313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,882 control chromosomes in the GnomAD database, including 25,375 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 0.56 (25375 hom., cov: 34)
• Consequence: ENSG00000290796 ENST00000444995.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 5 publications found

Genes affected

ENSG00000290796 (HGNC:):

LRP5L (HGNC:25323): (LDL receptor related protein 5 like (pseudogene)) Predicted to enable coreceptor activity. Predicted to be involved in several processes, including animal organ development; cholesterol homeostasis; and osteoblast development. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444995.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290796	ENST00000444995.7	TSL:5	n.176+2313C>T		intron	N/A
	ENSG00000290796	ENST00000650168.1		n.176+2313C>T		intron	N/A
	LRP5L	ENST00000650500.2		n.73+2313C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84818 AN: 151762 Hom.: 25363 Cov.: 34

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.559 AC: 84843 AN: 151882 Hom.: 25375 Cov.: 34 AF XY: 0.565 AC XY: 41908 AN XY: 74224

African (AFR) AF: 0.328 AC: 13579 AN: 41376

American (AMR) AF: 0.608 AC: 9283 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2294 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4496 AN: 5162

South Asian (SAS) AF: 0.766 AC: 3688 AN: 4812

European-Finnish (FIN) AF: 0.638 AC: 6738 AN: 10568

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42839 AN: 67914

Other (OTH) AF: 0.601 AC: 1266 AN: 2108

Alfa AF: 0.618 Hom.: 13171

Bravo AF: 0.543

Asia WGS AF: 0.768 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs84486; hg19: chr22-25798856;