rs76966965
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004104.5(FASN):c.6164-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,599,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004104.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.6164-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000306749.4 | |||
FASN | XM_011523538.3 | c.6164-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6164-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004104.5 | P1 | |||
FASN | ENST00000634990.1 | c.6158-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150928Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 228900Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126916
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1448160Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 719894
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150928Hom.: 0 Cov.: 30 AF XY: 0.0000272 AC XY: 2AN XY: 73654
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at