dbSNP rs1563353: LYPLAL1-AS1:n.61-9844T>C (chr1-219479684-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 ENST00000811290.1(LYPLAL1-AS1):n.61-9844T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,090 control chromosomes in the GnomAD database, including 38,259 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 0.71 ( 38259 hom., cov: 32)

Consequence

LYPLAL1-AS1
ENST00000811290.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Publications

9 publications found

Variant links:

Genes affected

LYPLAL1-AS1 (HGNC:54054): (LYPLAL1 antisense RNA 1)

LYPLAL1-AS1 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1 link	n.135-9841T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LYPLAL1-AS1	ENST00000811290.1 link	n.61-9844T>C	intron_variant	Intron 1 of 2
LYPLAL1-AS1	ENST00000811291.1 link	n.120-9841T>C	intron_variant	Intron 1 of 3
LYPLAL1-AS1	ENST00000811292.1 link	n.98-9841T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107645

AN:

151972

Hom.:

38229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.904

Gnomad AMR

AF:

0.680

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.833

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.694

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.714

Gnomad OTH

AF:

0.734

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.708

AC:

107729

AN:

152090

Hom.:

38259

Cov.:

AF XY:

0.710

AC XY:

52753

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.678

AC:

28109

AN:

41474

American (AMR)

AF:

0.681

AC:

10403

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.742

AC:

2575

AN:

3470

East Asian (EAS)

AF:

0.833

AC:

4303

AN:

5168

South Asian (SAS)

AF:

0.800

AC:

3857

AN:

4820

European-Finnish (FIN)

AF:

0.694

AC:

7336

AN:

10564

Middle Eastern (MID)

AF:

0.738

AC:

217

AN:

294

European-Non Finnish (NFE)

AF:

0.714

AC:

48547

AN:

67994

Other (OTH)

AF:

0.738

AC:

1558

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1654

3309

4963

6618

8272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.708

Hom.:

4470

Bravo

AF:

0.704

Asia WGS

AF:

0.810

AC:

2819

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.45

(source)

DANN

Benign

0.68

PhyloP100

-1.2

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over