rs143485066
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004104.5(FASN):c.7167G>A(p.Pro2389=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,601,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000086 ( 0 hom. )
Consequence
FASN
NM_004104.5 synonymous
NM_004104.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.31
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 17-82079588-C-T is Benign according to our data. Variant chr17-82079588-C-T is described in ClinVar as [Benign]. Clinvar id is 462106.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.31 with no splicing effect.
BS2
?
High AC in GnomAd4 at 129 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.7167G>A | p.Pro2389= | synonymous_variant | 42/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.7167G>A | p.Pro2389= | synonymous_variant | 42/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.7167G>A | p.Pro2389= | synonymous_variant | 42/43 | 1 | NM_004104.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000848 AC: 129AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000208 AC: 49AN: 235034Hom.: 0 AF XY: 0.000162 AC XY: 21AN XY: 129316
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GnomAD4 exome AF: 0.0000863 AC: 125AN: 1449058Hom.: 0 Cov.: 37 AF XY: 0.0000749 AC XY: 54AN XY: 721234
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GnomAD4 genome ? AF: 0.000847 AC: 129AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000886 AC XY: 66AN XY: 74472
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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 | Nov 27, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at