dbSNP rs4822622: 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

new If you want to explore the variant's impact on the transcript ENST00000467672.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467672.5. 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000290796	ENST00000467672.5	TSL:1	n.2362G>A	non_coding_transcript_exon	Exon 1 of 4
ENSG00000290796	ENST00000444995.7	TSL:5	n.598G>A	non_coding_transcript_exon	Exon 4 of 7
ENSG00000290796	ENST00000468442.1	TSL:3	n.486G>A	non_coding_transcript_exon	Exon 4 of 4

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over