chr17-82086437-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP3BP6_Very_StrongBS2
The NM_004104.5(FASN):c.3549G>A(p.Ser1183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,611,992 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00050 ( 1 hom. )
Consequence
FASN
NM_004104.5 synonymous
NM_004104.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.79
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.
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BP6
Variant 17-82086437-C-T is Benign according to our data. Variant chr17-82086437-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 462037.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 70 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.3549G>A | p.Ser1183= | synonymous_variant | 22/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.3549G>A | p.Ser1183= | synonymous_variant | 22/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.3549G>A | p.Ser1183= | synonymous_variant | 22/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.3549G>A | p.Ser1183= | synonymous_variant | 22/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000437 AC: 107AN: 245076Hom.: 0 AF XY: 0.000426 AC XY: 57AN XY: 133668
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GnomAD4 exome AF: 0.000504 AC: 736AN: 1459636Hom.: 1 Cov.: 35 AF XY: 0.000508 AC XY: 369AN XY: 726152
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GnomAD4 genome AF: 0.000459 AC: 70AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000577 AC XY: 43AN XY: 74500
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | FASN: BP7 - |
Computational scores
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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
DS_AG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at