Variant 22-25360196-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 ENST00000467672.5(ENSG00000290796):n.2362G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0283 in 1,505,550 control chromosomes in the GnomAD database, including 3,647 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 0.045 ( 532 hom., cov: 32)

Exomes 𝑓: 0.026 ( 3115 hom. )

Consequence

ENST00000467672.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.16

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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.629G>A		non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650168.1 linkuse as main transcript	n.730G>A		non_coding_transcript_exon_variant	5/8
LRP5L	ENST00000650500.2 linkuse as main transcript	n.627G>A		non_coding_transcript_exon_variant	5/8

Frequencies

GnomAD3 genomes

AF:

0.0444

AC:

6737

AN:

151762

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0446

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.0574

Gnomad FIN

AF:

0.00509

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00970

Gnomad OTH

AF:

0.0640

GnomAD4 exome

AF:

0.0265

AC:

35843

AN:

1353670

Hom.:

3115

Cov.:

AF XY:

0.0263

AC XY:

17583

AN XY:

669276

show subpopulations

Gnomad4 AFR exome

AF:

0.0463

Gnomad4 AMR exome

AF:

0.231

Gnomad4 ASJ exome

AF:

0.0225

Gnomad4 EAS exome

AF:

0.284

Gnomad4 SAS exome

AF:

0.0503

Gnomad4 FIN exome

AF:

0.00854

Gnomad4 NFE exome

AF:

0.00760

Gnomad4 OTH exome

AF:

0.0408

GnomAD4 genome

AF:

0.0445

AC:

6763

AN:

151880

Hom.:

532

Cov.:

AF XY:

0.0472

AC XY:

3508

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.0446

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.0242

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.0572

Gnomad4 FIN

AF:

0.00509

Gnomad4 NFE

AF:

0.00970

Gnomad4 OTH

AF:

0.0686

Alfa

AF:

0.0263

Hom.:

269

Bravo

AF:

0.0595

Asia WGS

AF:

0.162

AC:

563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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