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GeneBe

1-150966842-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_022075.5(CERS2):c.762C>T(p.Tyr254=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00379 in 1,613,740 control chromosomes in the GnomAD database, including 225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 120 hom., cov: 31)
Exomes 𝑓: 0.0021 ( 105 hom. )

Consequence

CERS2
NM_022075.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.274
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 -15 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=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-150966842-G-A is Benign according to our data. Variant chr1-150966842-G-A is described in ClinVar as [Benign]. Clinvar id is 780785.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=-0.274 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CERS2NM_022075.5 linkuse as main transcriptc.762C>T p.Tyr254= synonymous_variant 9/11 ENST00000368954.10
CERS2NM_181746.4 linkuse as main transcriptc.762C>T p.Tyr254= synonymous_variant 9/11
CERS2XM_011509451.3 linkuse as main transcriptc.822C>T p.Tyr274= synonymous_variant 9/11
CERS2XM_011509452.4 linkuse as main transcriptc.762C>T p.Tyr254= synonymous_variant 9/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CERS2ENST00000368954.10 linkuse as main transcriptc.762C>T p.Tyr254= synonymous_variant 9/111 NM_022075.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0200
AC:
3049
AN:
152090
Hom.:
119
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0693
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00844
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0167
GnomAD3 exomes
AF:
0.00534
AC:
1343
AN:
251474
Hom.:
42
AF XY:
0.00375
AC XY:
510
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.0705
Gnomad AMR exome
AF:
0.00474
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000123
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.00209
AC:
3050
AN:
1461532
Hom.:
105
Cov.:
32
AF XY:
0.00182
AC XY:
1320
AN XY:
727084
show subpopulations
Gnomad4 AFR exome
AF:
0.0704
Gnomad4 AMR exome
AF:
0.00525
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000186
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000118
Gnomad4 OTH exome
AF:
0.00497
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0201
AC:
3059
AN:
152208
Hom.:
120
Cov.:
31
AF XY:
0.0191
AC XY:
1418
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0693
Gnomad4 AMR
AF:
0.00843
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0166
Alfa
AF:
0.00687
Hom.:
43
Bravo
AF:
0.0234
Asia WGS
AF:
0.00404
AC:
15
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000178

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
-0.66
Cadd
Benign
1.1
Dann
Benign
0.85
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs9435954; hg19: chr1-150939318; API