Variant 22-25365969-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000650168.1(ENSG00000290796):n.703-5746G>A variant causes a intron, non coding transcript 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

ENST00000650168.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.72

Variant links:

Genes affected

(HGNC:):

links:

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]

LRP5L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LRP5L	XR_005228030.2 linkuse as main transcript	n.602-5746G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
	ENST00000650168.1 linkuse as main transcript	n.703-5746G>A	intron_variant, non_coding_transcript_variant
LRP5L	ENST00000650500.2 linkuse as main transcript	n.600-5746G>A	intron_variant, non_coding_transcript_variant
	ENST00000444995.7 linkuse as main transcript	n.571-5746G>A	intron_variant, non_coding_transcript_variant	5
	ENST00000468442.1 linkuse as main transcript	n.348-4650G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

116067

AN:

151806

Hom.:

45008

Cov.:

show subpopulations

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.:

AF XY:

0.764

AC XY:

56735

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.907

Gnomad4 AMR

AF:

0.694

Gnomad4 ASJ

AF:

0.655

Gnomad4 EAS

AF:

0.859

Gnomad4 SAS

AF:

0.864

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.697

Gnomad4 OTH

AF:

0.764

Alfa

AF:

0.730

Hom.:

18566

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

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over