rs146570982
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004104.5(FASN):c.6477C>T(p.Ser2159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,563,060 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00069 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00056 ( 12 hom. )
Consequence
FASN
NM_004104.5 synonymous
NM_004104.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.58
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 17-82081282-G-A is Benign according to our data. Variant chr17-82081282-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 531159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.58 with no splicing effect.
BS2
?
High AC in GnomAd4 at 105 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.6477C>T | p.Ser2159= | synonymous_variant | 38/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.6477C>T | p.Ser2159= | synonymous_variant | 38/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6477C>T | p.Ser2159= | synonymous_variant | 38/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.6471C>T | p.Ser2157= | synonymous_variant | 38/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000690 AC: 105AN: 152242Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00119 AC: 203AN: 170680Hom.: 2 AF XY: 0.00108 AC XY: 99AN XY: 91480
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GnomAD4 exome AF: 0.000558 AC: 787AN: 1410818Hom.: 12 Cov.: 36 AF XY: 0.000578 AC XY: 403AN XY: 697128
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GnomAD4 genome ? AF: 0.000690 AC: 105AN: 152242Hom.: 1 Cov.: 33 AF XY: 0.000619 AC XY: 46AN XY: 74370
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | FASN: BP4, BP7 - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at