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GeneBe

1-150967832-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_022075.5(CERS2):c.456C>T(p.Ala152=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,613,552 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0085 ( 7 hom., cov: 32)
Exomes 𝑓: 0.011 ( 113 hom. )

Consequence

CERS2
NM_022075.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.27
Variant links:
Genes affected
CERS2 (HGNC:14076): (ceramide synthase 2) This gene encodes a protein that has sequence similarity to yeast longevity assurance gene 1. Mutation or overexpression of the related gene in yeast has been shown to alter yeast lifespan. The human protein may play a role in the regulation of cell growth. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-150967832-G-A is Benign according to our data. Variant chr1-150967832-G-A is described in ClinVar as [Benign]. Clinvar id is 770856.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.27 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 1288 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CERS2NM_022075.5 linkuse as main transcriptc.456C>T p.Ala152= synonymous_variant 5/11 ENST00000368954.10
CERS2NM_181746.4 linkuse as main transcriptc.456C>T p.Ala152= synonymous_variant 5/11
CERS2XM_011509451.3 linkuse as main transcriptc.516C>T p.Ala172= synonymous_variant 5/11
CERS2XM_011509452.4 linkuse as main transcriptc.456C>T p.Ala152= synonymous_variant 5/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CERS2ENST00000368954.10 linkuse as main transcriptc.456C>T p.Ala152= synonymous_variant 5/111 NM_022075.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00847
AC:
1288
AN:
152118
Hom.:
7
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00229
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0103
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00767
Gnomad FIN
AF:
0.00217
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0120
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00914
AC:
2298
AN:
251430
Hom.:
27
AF XY:
0.00965
AC XY:
1311
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.00191
Gnomad AMR exome
AF:
0.00682
Gnomad ASJ exome
AF:
0.0376
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00751
Gnomad FIN exome
AF:
0.00328
Gnomad NFE exome
AF:
0.0113
Gnomad OTH exome
AF:
0.0112
GnomAD4 exome
AF:
0.0113
AC:
16573
AN:
1461316
Hom.:
113
Cov.:
32
AF XY:
0.0114
AC XY:
8291
AN XY:
726994
show subpopulations
Gnomad4 AFR exome
AF:
0.00248
Gnomad4 AMR exome
AF:
0.00771
Gnomad4 ASJ exome
AF:
0.0396
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00765
Gnomad4 FIN exome
AF:
0.00281
Gnomad4 NFE exome
AF:
0.0121
Gnomad4 OTH exome
AF:
0.0120
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00847
AC:
1289
AN:
152236
Hom.:
7
Cov.:
32
AF XY:
0.00822
AC XY:
612
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.00229
Gnomad4 AMR
AF:
0.0103
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.00789
Gnomad4 FIN
AF:
0.00217
Gnomad4 NFE
AF:
0.0120
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.0127
Hom.:
23
Bravo
AF:
0.00904
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.0127
EpiControl
AF:
0.0120

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
4.8
Dann
Benign
0.80
RBP_binding_hub_radar
1.0
RBP_regulation_power_radar
2.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs76805488; hg19: chr1-150940308; COSMIC: COSV99644393; COSMIC: COSV99644393; API