chr1-150966842-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
NM_022075.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.274
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
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
?
Synonymous conserved (PhyloP=-0.274 with no splicing effect.
BA1
?
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 |
---|---|---|---|---|---|---|---|
CERS2 | NM_022075.5 | c.762C>T | p.Tyr254= | synonymous_variant | 9/11 | ENST00000368954.10 | |
CERS2 | NM_181746.4 | c.762C>T | p.Tyr254= | synonymous_variant | 9/11 | ||
CERS2 | XM_011509451.3 | c.822C>T | p.Tyr274= | synonymous_variant | 9/11 | ||
CERS2 | XM_011509452.4 | c.762C>T | p.Tyr254= | synonymous_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS2 | ENST00000368954.10 | c.762C>T | p.Tyr254= | synonymous_variant | 9/11 | 1 | NM_022075.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0200 AC: 3049AN: 152090Hom.: 119 Cov.: 31
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GnomAD3 exomes AF: 0.00534 AC: 1343AN: 251474Hom.: 42 AF XY: 0.00375 AC XY: 510AN XY: 135914
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GnomAD4 exome AF: 0.00209 AC: 3050AN: 1461532Hom.: 105 Cov.: 32 AF XY: 0.00182 AC XY: 1320AN XY: 727084
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GnomAD4 genome ? AF: 0.0201 AC: 3059AN: 152208Hom.: 120 Cov.: 31 AF XY: 0.0191 AC XY: 1418AN XY: 74422
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at