chr1-150967407-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022075.5(CERS2):c.597T>C(p.Ser199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,598,534 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 7 hom., cov: 32)
Exomes 𝑓: 0.011 ( 106 hom. )
Consequence
CERS2
NM_022075.5 synonymous
NM_022075.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.374
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 1-150967407-A-G is Benign according to our data. Variant chr1-150967407-A-G is described in ClinVar as [Benign]. Clinvar id is 770855.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.374 with no splicing effect.
BS2
?
High AC in GnomAd at 1285 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERS2 | NM_022075.5 | c.597T>C | p.Ser199= | synonymous_variant | 7/11 | ENST00000368954.10 | |
CERS2 | NM_181746.4 | c.597T>C | p.Ser199= | synonymous_variant | 7/11 | ||
CERS2 | XM_011509451.3 | c.657T>C | p.Ser219= | synonymous_variant | 7/11 | ||
CERS2 | XM_011509452.4 | c.597T>C | p.Ser199= | synonymous_variant | 7/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS2 | ENST00000368954.10 | c.597T>C | p.Ser199= | synonymous_variant | 7/11 | 1 | NM_022075.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00844 AC: 1285AN: 152164Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00912 AC: 2292AN: 251442Hom.: 27 AF XY: 0.00961 AC XY: 1306AN XY: 135904
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GnomAD4 exome AF: 0.0112 AC: 16207AN: 1446252Hom.: 106 Cov.: 30 AF XY: 0.0113 AC XY: 8140AN XY: 720510
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GnomAD4 genome ? AF: 0.00844 AC: 1286AN: 152282Hom.: 7 Cov.: 32 AF XY: 0.00821 AC XY: 611AN XY: 74462
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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 submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at