Variant 11-76926686-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018367.7(ACER3):c.214+19C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,451,712 control chromosomes in the GnomAD database, including 345,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 27907 hom., cov: 31)

Exomes 𝑓: 0.69 ( 317612 hom. )

Consequence

ACER3
NM_018367.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0550

Variant links:

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 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 11-76926686-C-G is Benign according to our data. Variant chr11-76926686-C-G is described in ClinVar as [Benign]. Clinvar id is 1170184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACER3	NM_018367.7 linkuse as main transcript	c.214+19C>G		intron_variant		ENST00000532485.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACER3	ENST00000532485.6 linkuse as main transcript	c.214+19C>G		intron_variant		1	NM_018367.7	P1	Q9NUN7-1

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86323

AN:

151854

Hom.:

27908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.721

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.712

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.580

GnomAD3 exomes

AF:

0.627

AC:

144082

AN:

229692

Hom.:

48085

AF XY:

0.643

AC XY:

80048

AN XY:

124456

show subpopulations

Gnomad AFR exome

AF:

0.227

Gnomad AMR exome

AF:

0.417

Gnomad ASJ exome

AF:

0.723

Gnomad EAS exome

AF:

0.611

Gnomad SAS exome

AF:

0.613

Gnomad FIN exome

AF:

0.708

Gnomad NFE exome

AF:

0.726

Gnomad OTH exome

AF:

0.645

GnomAD4 exome

AF:

0.691

AC:

898638

AN:

1299742

Hom.:

317612

Cov.:

AF XY:

0.694

AC XY:

453119

AN XY:

653274

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.432

Gnomad4 ASJ exome

AF:

0.724

Gnomad4 EAS exome

AF:

0.632

Gnomad4 SAS exome

AF:

0.622

Gnomad4 FIN exome

AF:

0.709

Gnomad4 NFE exome

AF:

0.725

Gnomad4 OTH exome

AF:

0.662

GnomAD4 genome

AF:

0.568

AC:

86332

AN:

151970

Hom.:

27907

Cov.:

AF XY:

0.565

AC XY:

41958

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.513

Gnomad4 ASJ

AF:

0.721

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.620

Gnomad4 FIN

AF:

0.712

Gnomad4 NFE

AF:

0.737

Gnomad4 OTH

AF:

0.583

Alfa

AF:

0.614

Hom.:

4079

Bravo

AF:

0.543

Asia WGS

AF:

0.559

AC:

1943

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.2

DANN

Benign

0.47

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

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