NM_018367.7:c.36C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_018367.7(ACER3):c.36C>T(p.Gly12Gly) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACER3
NM_018367.7 synonymous
NM_018367.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.407
Publications
0 publications found
Genes affected
ACER3 (HGNC:16066): (alkaline ceramidase 3) Enables N-acylsphingosine amidohydrolase activity and metal ion binding activity. Involved in several processes, including myelination; positive regulation of cell population proliferation; and sphingolipid metabolic process. Is integral component of Golgi membrane and integral component of endoplasmic reticulum membrane. Biomarker of hepatocellular carcinoma and non-alcoholic steatohepatitis. [provided by Alliance of Genome Resources, Apr 2022]
ACER3 Gene-Disease associations (from GenCC):
- alkaline ceramidase 3 deficiencyInheritance: Unknown, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 11-76861012-C-T is Benign according to our data. Variant chr11-76861012-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3683041.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.407 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018367.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ACER3 | TSL:1 MANE Select | c.36C>T | p.Gly12Gly | synonymous | Exon 1 of 11 | ENSP00000434480.1 | Q9NUN7-1 | ||
| ACER3 | TSL:1 | n.36C>T | non_coding_transcript_exon | Exon 1 of 11 | ENSP00000278544.5 | J3KN85 | |||
| ACER3 | TSL:1 | n.36C>T | non_coding_transcript_exon | Exon 1 of 11 | ENSP00000432109.1 | E9PKR3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1394434Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 687868
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1394434
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
687868
African (AFR)
AF:
AC:
0
AN:
31366
American (AMR)
AF:
AC:
0
AN:
35604
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25094
East Asian (EAS)
AF:
AC:
0
AN:
35582
South Asian (SAS)
AF:
AC:
0
AN:
78996
European-Finnish (FIN)
AF:
AC:
0
AN:
48048
Middle Eastern (MID)
AF:
AC:
0
AN:
4086
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1077930
Other (OTH)
AF:
AC:
0
AN:
57728
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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