19-15878940-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001082.5(CYP4F2):c.1398-4C>G 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 0.000836 in 149,520 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 Benign (★).
Frequency
Consequence
NM_001082.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F2 | NM_001082.5 | c.1398-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.1398-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001082.5 | P3 | |||
CYP4F2 | ENST00000011989.11 | c.1398-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
CYP4F2 | ENST00000589654.2 | c.186-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
CYP4F2 | ENST00000392846.7 | n.1341-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000837 AC: 125AN: 149410Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00346 AC: 858AN: 247838Hom.: 0 AF XY: 0.00223 AC XY: 299AN XY: 134196
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000605 AC: 880AN: 1454958Hom.: 0 Cov.: 39 AF XY: 0.000529 AC XY: 383AN XY: 724066
GnomAD4 genome AF: 0.000836 AC: 125AN: 149520Hom.: 0 Cov.: 34 AF XY: 0.000807 AC XY: 59AN XY: 73122
ClinVar
Submissions by phenotype
CYP4F2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at