rs2228309
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004104.5(FASN):āc.567T>Cā(p.Asn189=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 1,596,526 control chromosomes in the GnomAD database, including 239,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.51 ( 20291 hom., cov: 34)
Exomes š: 0.54 ( 218728 hom. )
Consequence
FASN
NM_004104.5 synonymous
NM_004104.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.70
Genes affected
FASN (HGNC:3594): (fatty acid synthase) The enzyme encoded by this gene is a multifunctional protein. Its main function is to catalyze the synthesis of palmitate from acetyl-CoA and malonyl-CoA, in the presence of NADPH, into long-chain saturated fatty acids. In some cancer cell lines, this protein has been found to be fused with estrogen receptor-alpha (ER-alpha), in which the N-terminus of FAS is fused in-frame with the C-terminus of ER-alpha. [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=-0.75).
BP6
?
Variant 17-82093307-A-G is Benign according to our data. Variant chr17-82093307-A-G is described in ClinVar as [Benign]. Clinvar id is 1170035.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-82093307-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=1.7 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.567T>C | p.Asn189= | synonymous_variant | 5/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.567T>C | p.Asn189= | synonymous_variant | 5/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.567T>C | p.Asn189= | synonymous_variant | 5/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.567T>C | p.Asn189= | synonymous_variant | 5/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.508 AC: 77245AN: 152042Hom.: 20289 Cov.: 34
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GnomAD3 exomes AF: 0.463 AC: 102735AN: 221732Hom.: 25640 AF XY: 0.470 AC XY: 56296AN XY: 119800
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GnomAD4 exome AF: 0.542 AC: 782135AN: 1444366Hom.: 218728 Cov.: 57 AF XY: 0.538 AC XY: 385474AN XY: 716888
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GnomAD4 genome ? AF: 0.508 AC: 77265AN: 152160Hom.: 20291 Cov.: 34 AF XY: 0.502 AC XY: 37342AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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