dbSNP rs13263637: ASAH1-AS1:n.483+4239T>G (chr8-18091376-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000499554.6(ASAH1-AS1):n.483+4239T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,996 control chromosomes in the GnomAD database, including 13,952 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 0.40 ( 13952 hom., cov: 32)

Consequence

ASAH1-AS1
ENST00000499554.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Publications

4 publications found

Variant links:

Genes affected

ASAH1-AS1 (HGNC:55603): (ASAH1 antisense RNA 1)

ASAH1-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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASAH1-AS1	NR_125429.1 link	n.483+4239T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ASAH1-AS1	ENST00000499554.6 link	n.483+4239T>G	intron_variant	Intron 4 of 4	3
ASAH1-AS1	ENST00000521775.6 link	n.1129+4440T>G	intron_variant	Intron 2 of 2	4
ASAH1-AS1	ENST00000649327.1 link	n.549+4440T>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60426

AN:

151878

Hom.:

13954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.520

Gnomad OTH

AF:

0.431

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

GnomAD4 genome

AF:

0.398

AC:

60423

AN:

151996

Hom.:

13952

Cov.:

AF XY:

0.397

AC XY:

29484

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.155

AC:

6410

AN:

41440

American (AMR)

AF:

0.427

AC:

6520

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

1457

AN:

3460

East Asian (EAS)

AF:

0.373

AC:

1930

AN:

5168

South Asian (SAS)

AF:

0.416

AC:

2007

AN:

4824

European-Finnish (FIN)

AF:

0.504

AC:

5323

AN:

10562

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.520

AC:

35339

AN:

67972

Other (OTH)

AF:

0.429

AC:

907

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1694

3389

5083

6778

8472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.474

Hom.:

13429

Bravo

AF:

0.384

Asia WGS

AF:

0.368

AC:

1282

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.2

(source)

DANN

Benign

0.74

PhyloP100

0.014

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