dbSNP rs133201: ENSG00000290796:n.1257T>C (chr22-25361301-A-G) – 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.1257T>C 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 151,888 control chromosomes in the GnomAD database, including 45,140 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 ( 45117 hom., cov: 33)

Exomes 𝑓: 0.77 ( 23 hom. )

Consequence

ENSG00000290796
ENST00000467672.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300

Publications

10 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LRP5L	XR_005228024.2 link	n.1692T>C	non_coding_transcript_exon_variant	Exon 4 of 7
LRP5L	XR_007068027.1 link	n.1669T>C	non_coding_transcript_exon_variant	Exon 4 of 7
LRP5L	XR_007068028.1 link	n.1692T>C	non_coding_transcript_exon_variant	Exon 4 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290796	ENST00000467672.5 link	n.1257T>C	non_coding_transcript_exon_variant	Exon 1 of 4	1
ENSG00000290796	ENST00000468442.1 link	n.366T>C	non_coding_transcript_exon_variant	Exon 3 of 4	3
ENSG00000290796	ENST00000444995.7 link	n.571-1078T>C	intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

116007

AN:

151696

Hom.:

45048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.916

Gnomad AMI

AF:

0.647

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.821

Gnomad SAS

AF:

0.864

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.657

Gnomad NFE

AF:

0.696

Gnomad OTH

AF:

0.759

GnomAD4 exome

AF:

0.770

AC:

AN:

Hom.:

Cov.:

AF XY:

0.808

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.731

AC:

AN:

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.580

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.765

AC:

116136

AN:

151814

Hom.:

45117

Cov.:

AF XY:

0.764

AC XY:

56692

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.916

AC:

37923

AN:

41384

American (AMR)

AF:

0.685

AC:

10443

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.655

AC:

2273

AN:

3472

East Asian (EAS)

AF:

0.822

AC:

4229

AN:

5142

South Asian (SAS)

AF:

0.864

AC:

4148

AN:

4802

European-Finnish (FIN)

AF:

0.706

AC:

7461

AN:

10574

Middle Eastern (MID)

AF:

0.669

AC:

194

AN:

290

European-Non Finnish (NFE)

AF:

0.696

AC:

47276

AN:

67892

Other (OTH)

AF:

0.760

AC:

1599

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1280

2560

3840

5120

6400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.709

Hom.:

65498

Bravo

AF:

0.769

Asia WGS

AF:

0.852

AC:

2965

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.63

PhyloP100

0.030

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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