Genetic Variant ENSG00000290796:n.2362G>A (chr22-25360196-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

ENSG00000290796
ENST00000467672.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.16

Publications

7 publications found

Variant links:

Genes affected

ENSG00000290796 (HGNC:):

ENSG00000290796 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 was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank
LRP5L	XR_005228024.2 link	n.2797G>A	non_coding_transcript_exon_variant	Exon 4 of 7
LRP5L	XR_005228030.2 link	n.629G>A	non_coding_transcript_exon_variant	Exon 4 of 7
LRP5L	XR_007068026.1 link	n.629G>A	non_coding_transcript_exon_variant	Exon 4 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290796	ENST00000467672.5 link	n.2362G>A	non_coding_transcript_exon_variant	Exon 1 of 4	1
ENSG00000290796	ENST00000444995.7 link	n.598G>A	non_coding_transcript_exon_variant	Exon 4 of 7	5
ENSG00000290796	ENST00000468442.1 link	n.486G>A	non_coding_transcript_exon_variant	Exon 4 of 4	3

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

African (AFR)

AF:

0.0463

AC:

1447

AN:

31244

American (AMR)

AF:

0.231

AC:

8769

AN:

37994

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

522

AN:

23162

East Asian (EAS)

AF:

0.284

AC:

10468

AN:

36890

South Asian (SAS)

AF:

0.0503

AC:

3797

AN:

75462

European-Finnish (FIN)

AF:

0.00854

AC:

384

AN:

44988

Middle Eastern (MID)

AF:

0.0457

AC:

229

AN:

5016

European-Non Finnish (NFE)

AF:

0.00760

AC:

7921

AN:

1042332

Other (OTH)

AF:

0.0408

AC:

2306

AN:

56582

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

1406

2812

4218

5624

7030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

544

1088

1632

2176

2720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0445

AC:

6763

AN:

151880

Hom.:

532

Cov.:

AF XY:

0.0472

AC XY:

3508

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.0446

AC:

1845

AN:

41392

American (AMR)

AF:

0.144

AC:

2204

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.0242

AC:

AN:

3468

East Asian (EAS)

AF:

0.291

AC:

1492

AN:

5130

South Asian (SAS)

AF:

0.0572

AC:

274

AN:

4788

European-Finnish (FIN)

AF:

0.00509

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00970

AC:

659

AN:

67936

Other (OTH)

AF:

0.0686

AC:

144

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

268

537

805

1074

1342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0302

Hom.:

411

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

(source)

DANN

Benign

0.63

PhyloP100

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over