rs761723139
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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.4059C>T(p.Leu1353=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 1,595,834 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
FASN
NM_004104.5 synonymous
NM_004104.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
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=-0.78).
BP6
?
Variant 17-82085545-G-A is Benign according to our data. Variant chr17-82085545-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 531066.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.83 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.4059C>T | p.Leu1353= | synonymous_variant | 23/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.4059C>T | p.Leu1353= | synonymous_variant | 23/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.4059C>T | p.Leu1353= | synonymous_variant | 23/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.4053C>T | p.Leu1351= | synonymous_variant | 23/43 | 5 | |||
FASN | ENST00000579410.1 | n.116C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000232 AC: 5AN: 215870Hom.: 0 AF XY: 0.0000171 AC XY: 2AN XY: 117176
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GnomAD4 exome AF: 0.0000166 AC: 24AN: 1443610Hom.: 0 Cov.: 67 AF XY: 0.0000181 AC XY: 13AN XY: 716570
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74372
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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