dbSNP rs11216158: APOA1-AS:n.123+4395G>A (chr11-116840634-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444200.2(APOA1-AS):n.123+4395G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,236 control chromosomes in the GnomAD database, including 2,835 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 0.18 ( 2835 hom., cov: 33)

Consequence

APOA1-AS
ENST00000444200.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553

Publications

9 publications found

Variant links:

Genes affected

APOA1-AS (HGNC:40079): (APOA1 antisense RNA)

APOA1-AS 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 = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA1-AS	NR_126362.1 link	n.123+4395G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOA1-AS	ENST00000444200.2 link	n.123+4395G>A		intron_variant	Intron 1 of 1	4
APOA1-AS	ENST00000669664.1 link	n.74+4395G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27616

AN:

152118

Hom.:

2817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.172

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

GnomAD4 genome

AF:

0.182

AC:

27692

AN:

152236

Hom.:

2835

Cov.:

AF XY:

0.181

AC XY:

13470

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.266

AC:

11048

AN:

41540

American (AMR)

AF:

0.204

AC:

3120

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

389

AN:

3472

East Asian (EAS)

AF:

0.258

AC:

1338

AN:

5178

South Asian (SAS)

AF:

0.201

AC:

970

AN:

4828

European-Finnish (FIN)

AF:

0.119

AC:

1266

AN:

10610

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9014

AN:

67994

Other (OTH)

AF:

0.175

AC:

370

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1168

2336

3504

4672

5840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.157

Hom.:

3039

Bravo

AF:

0.194

Asia WGS

AF:

0.232

AC:

806

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

0.48

(source)

DANN

Benign

0.49

PhyloP100

-0.55

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