dbSNP rs17126232: ASAH1-AS1:n.405-6699C>T (chr8-18120141-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 ENST00000659561.2(ASAH1-AS1):n.405-6699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,164 control chromosomes in the GnomAD database, including 884 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 0.11 ( 884 hom., cov: 32)

Consequence

ASAH1-AS1
ENST00000659561.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.614

Publications

13 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ASAH1-AS1	ENST00000659561.2 link	n.405-6699C>T	intron_variant	Intron 4 of 4
ASAH1-AS1	ENST00000839452.1 link	n.611-6699C>T	intron_variant	Intron 2 of 2
ASAH1-AS1	ENST00000839453.1 link	n.703-6699C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15990

AN:

152046

Hom.:

880

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.114

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

GnomAD4 genome

AF:

0.105

AC:

16019

AN:

152164

Hom.:

884

Cov.:

AF XY:

0.108

AC XY:

8013

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.109

AC:

4544

AN:

41508

American (AMR)

AF:

0.106

AC:

1627

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

453

AN:

3468

East Asian (EAS)

AF:

0.00116

AC:

AN:

5172

South Asian (SAS)

AF:

0.104

AC:

503

AN:

4818

European-Finnish (FIN)

AF:

0.129

AC:

1365

AN:

10590

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7170

AN:

67990

Other (OTH)

AF:

0.112

AC:

237

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

746

1492

2238

2984

3730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.104

Hom.:

2584

Bravo

AF:

0.104

Asia WGS

AF:

0.0610

AC:

211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.78

(source)

DANN

Benign

0.32

PhyloP100

-0.61

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