chr22-25365969-C-T

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.

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290796	ENST00000444995.7	TSL:5	n.571-5746G>A		intron	N/A
	ENSG00000290796	ENST00000468442.1	TSL:3	n.348-4650G>A		intron	N/A
	ENSG00000290796	ENST00000650168.1		n.703-5746G>A		intron	N/A

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 v4.9

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;