rs10103355

Positions:

• chr8-18061425-A-C
• chr8-18061425-A-G
• chr8-18061425-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP4_Moderate

The NM_177924.5(ASAH1):​c.737T>G​(p.Val246Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V246A) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ASAH1 NM_177924.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a chain Acid ceramidase subunit beta (size 252) in uniprot entity ASAH1_HUMAN there are 5 pathogenic changes around while only 1 benign (83%) in NM_177924.5
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16687775).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASAH1	NM_177924.5	c.737T>G	p.Val246Gly	missense_variant	10/14	ENST00000637790.2	NP_808592.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASAH1	ENST00000637790.2	c.737T>G	p.Val246Gly	missense_variant	10/14	1	NM_177924.5	ENSP00000490272	P2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.85e-7 AC: 1 AN: 1460834 Hom.: 0 Cov.: 46 AF XY: 0.00 AC XY: 0 AN XY: 726846

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.073	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	19
DANN	Benign	0.81
DEOGEN2	Benign	0.39	T;T;T;.;T;T;T;T;T;T;T;.;.;.;.;T
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.49
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.24	.;T;T;T;T;.;T;T;T;T;T;T;T;T;T;T
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.17	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-1.4	N;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	0.13	P;P;P;P;P
PrimateAI	Benign	0.37	T
PROVEAN	Benign	4.2	.;N;N;N;.;.;.;.;.;.;.;.;.;.;N;.
REVEL	Benign	0.24
Sift	Benign	0.87	.;T;T;T;.;.;.;.;.;.;.;.;.;.;T;.
Sift4G	Benign	0.81	.;T;T;T;.;.;.;.;.;.;.;.;.;.;T;.
Polyphen		0.0	B;B;B;B;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.11, 0.11, 0.13, 0.14
MutPred		0.38		Loss of stability (P = 0.0572);Loss of stability (P = 0.0572);.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP		0.65
MPC		0.0027
ClinPred		0.17	T
GERP RS		3.3
Varity_R		0.065
gMVP		0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs10103355; hg19: chr8-17918934;