rs713847

Variant names:

• chr22-25365969-C-T
• rs713847
• XR_007068030.1:n.10062G>A

Variant summary

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

The XR_007068030.1(LRP5L):​n.10062G>A 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 151,924 control chromosomes in the GnomAD database, including 45,075 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 (45075 hom., cov: 34)
• Consequence: LRP5L XR_007068030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.72
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP5L	XR_007068030.1	n.10062G>A		non_coding_transcript_exon_variant	Exon 4 of 7
LRP5L	XR_007068031.1	n.10314G>A		non_coding_transcript_exon_variant	Exon 3 of 6
LRP5L	XR_005228024.2	n.602-3578G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290796	ENST00000444995.7	n.571-5746G>A		intron_variant	Intron 3 of 6	5
ENSG00000290796	ENST00000468442.1	n.348-4650G>A		intron_variant	Intron 2 of 3	3
ENSG00000290796	ENST00000650168.1	n.703-5746G>A		intron_variant	Intron 4 of 7
LRP5L	ENST00000650500.2	n.600-5746G>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116067 AN: 151806 Hom.: 45008 Cov.: 34

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.697

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: 116194 AN: 151924 Hom.: 45075 Cov.: 34 AF XY: 0.764 AC XY: 56735 AN XY: 74242

African (AFR) AF: 0.907 AC: 37608 AN: 41454

American (AMR) AF: 0.694 AC: 10593 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2271 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4435 AN: 5162

South Asian (SAS) AF: 0.864 AC: 4150 AN: 4804

European-Finnish (FIN) AF: 0.706 AC: 7445 AN: 10552

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47298 AN: 67904

Other (OTH) AF: 0.764 AC: 1608 AN: 2106

Alfa AF: 0.731 Hom.: 27473

Bravo AF: 0.769

Asia WGS AF: 0.868 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.046
DANN	Benign	0.75
PhyloP100		-4.7
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: rs713847; hg19: chr22-25761936;