XR_007068030.1:n.9988A>G

Variant names:

• chr22-25366043-T-C
• rs713878
• XR_007068030.1:n.9988A>G

Variant summary

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

The XR_007068030.1(LRP5L):​n.9988A>G 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 0.457 in 151,780 control chromosomes in the GnomAD database, including 16,740 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 0.46 (16740 hom., cov: 34)
• Consequence: LRP5L XR_007068030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 5 publications found

Genes affected

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]

ENSG00000290796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290796	ENST00000444995.7	TSL:5	n.571-5820A>G		intron	N/A
	ENSG00000290796	ENST00000468442.1	TSL:3	n.348-4724A>G		intron	N/A
	ENSG00000290796	ENST00000650168.1		n.703-5820A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69321 AN: 151662 Hom.: 16736 Cov.: 34

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.457 AC: 69341 AN: 151780 Hom.: 16740 Cov.: 34 AF XY: 0.457 AC XY: 33879 AN XY: 74174

African (AFR) AF: 0.290 AC: 11979 AN: 41378

American (AMR) AF: 0.376 AC: 5743 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2292 AN: 5136

South Asian (SAS) AF: 0.626 AC: 3005 AN: 4800

European-Finnish (FIN) AF: 0.510 AC: 5380 AN: 10546

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37456 AN: 67872

Other (OTH) AF: 0.486 AC: 1022 AN: 2104

Alfa AF: 0.515 Hom.: 9676

Bravo AF: 0.434

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.88
PhyloP100		-0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs713878; hg19: chr22-25762010;