rs12547845

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_177924.5(ASAH1):c.126-21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,467,130 control chromosomes in the GnomAD database, including 172,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 14933 hom., cov: 31)

Exomes 𝑓: 0.48 ( 157657 hom. )

Consequence

ASAH1
NM_177924.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.776

Variant links:

Genes affected

ASAH1 (HGNC:735): (N-acylsphingosine amidohydrolase 1) This gene encodes a member of the acid ceramidase family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. Processing of this preproprotein generates alpha and beta subunits that heterodimerize to form the mature lysosomal enzyme, which catalyzes the degradation of ceramide into sphingosine and free fatty acid. This enzyme is overexpressed in multiple human cancers and may play a role in cancer progression. Mutations in this gene are associated with the lysosomal storage disorder, Farber lipogranulomatosis, and a neuromuscular disorder, spinal muscular atrophy with progressive myoclonic epilepsy. [provided by RefSeq, Oct 2015]

ASAH1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 8-18071411-T-C is Benign according to our data. Variant chr8-18071411-T-C is described in ClinVar as [Benign]. Clinvar id is 259277.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASAH1	NM_177924.5 linkuse as main transcript	c.126-21A>G		intron_variant		ENST00000637790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAH1	ENST00000637790.2 linkuse as main transcript	c.126-21A>G		intron_variant		1	NM_177924.5	P2	Q13510-1

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65227

AN:

151782

Hom.:

14917

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.487

Gnomad OTH

AF:

0.465

GnomAD3 exomes

AF:

0.494

AC:

104458

AN:

211334

Hom.:

26750

AF XY:

0.497

AC XY:

56088

AN XY:

112832

show subpopulations

Gnomad AFR exome

AF:

0.272

Gnomad AMR exome

AF:

0.655

Gnomad ASJ exome

AF:

0.609

Gnomad EAS exome

AF:

0.366

Gnomad SAS exome

AF:

0.537

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.488

Gnomad OTH exome

AF:

0.502

GnomAD4 exome

AF:

0.485

AC:

637842

AN:

1315230

Hom.:

157657

Cov.:

AF XY:

0.488

AC XY:

320838

AN XY:

657758

show subpopulations

Gnomad4 AFR exome

AF:

0.266

Gnomad4 AMR exome

AF:

0.638

Gnomad4 ASJ exome

AF:

0.610

Gnomad4 EAS exome

AF:

0.403

Gnomad4 SAS exome

AF:

0.538

Gnomad4 FIN exome

AF:

0.412

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.430

AC:

65282

AN:

151900

Hom.:

14933

Cov.:

AF XY:

0.431

AC XY:

31960

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.529

Gnomad4 ASJ

AF:

0.619

Gnomad4 EAS

AF:

0.382

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.487

Gnomad4 OTH

AF:

0.461

Alfa

AF:

0.478

Hom.:

3344

Bravo

AF:

0.434

Asia WGS

AF:

0.418

AC:

1453

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 22, 2015	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Spinal muscular atrophy-progressive myoclonic epilepsy syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Farber lipogranulomatosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.0

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over