chr4-186191828-C-CGGGGCTCTGGCT
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_207352.4(CYP4V2):c.13_24dup(p.Trp5_Leu8dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000256 in 1,561,650 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
CYP4V2
NM_207352.4 inframe_insertion
NM_207352.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.163
Genes affected
CYP4V2 (HGNC:23198): (cytochrome P450 family 4 subfamily V member 2) This gene encodes a member of the cytochrome P450 hemethiolate protein superfamily which are involved in oxidizing various substrates in the metabolic pathway. It is implicated in the metabolism of fatty acid precursors into n-3 polyunsaturated fatty acids. Mutations in this gene result in Bietti crystalline corneoretinal dystrophy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_207352.4.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4V2 | NM_207352.4 | c.13_24dup | p.Trp5_Leu8dup | inframe_insertion | 1/11 | ENST00000378802.5 | |
CYP4V2 | XM_005262935.5 | c.13_24dup | p.Trp5_Leu8dup | inframe_insertion | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4V2 | ENST00000378802.5 | c.13_24dup | p.Trp5_Leu8dup | inframe_insertion | 1/11 | 1 | NM_207352.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000213 AC: 3AN: 1409556Hom.: 0 Cov.: 30 AF XY: 0.00000143 AC XY: 1AN XY: 697816
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74302
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 18, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with CYP4V2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.13_24dup, results in the insertion of 4 amino acid(s) of the CYP4V2 protein (p.Trp5_Leu8dup), but otherwise preserves the integrity of the reading frame. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at