rs4246444
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000306749.4(FASN):c.6595+88A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,475,934 control chromosomes in the GnomAD database, including 390,728 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.74 ( 42169 hom., cov: 34)
Exomes 𝑓: 0.72 ( 348559 hom. )
Consequence
FASN
ENST00000306749.4 intron
ENST00000306749.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.204
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.6595+88A>C | intron_variant | ENST00000306749.4 | NP_004095.4 | |||
FASN | XM_011523538.3 | c.6595+88A>C | intron_variant | XP_011521840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6595+88A>C | intron_variant | 1 | NM_004104.5 | ENSP00000304592 | P1 | |||
FASN | ENST00000634990.1 | c.6589+88A>C | intron_variant | 5 | ENSP00000488964 |
Frequencies
GnomAD3 genomes AF: 0.740 AC: 112502AN: 152022Hom.: 42120 Cov.: 34
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GnomAD4 exome AF: 0.722 AC: 955637AN: 1323794Hom.: 348559 Cov.: 22 AF XY: 0.715 AC XY: 469355AN XY: 656122
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GnomAD4 genome AF: 0.740 AC: 112607AN: 152140Hom.: 42169 Cov.: 34 AF XY: 0.736 AC XY: 54721AN XY: 74390
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ClinVar
Not reported inComputational 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at