chr4-186199057-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207352.4(CYP4V2):c.775C>A(p.Gln259Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 1,612,180 control chromosomes in the GnomAD database, including 310,979 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_207352.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CYP4V2 | NM_207352.4 | c.775C>A | p.Gln259Lys | missense_variant | Exon 6 of 11 | ENST00000378802.5 | NP_997235.3 | |
CYP4V2 | XM_005262935.5 | c.775C>A | p.Gln259Lys | missense_variant | Exon 6 of 11 | XP_005262992.1 | ||
CYP4V2 | XM_047450077.1 | c.379C>A | p.Gln127Lys | missense_variant | Exon 4 of 9 | XP_047306033.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.606 AC: 92014AN: 151902Hom.: 28197 Cov.: 32
GnomAD3 exomes AF: 0.573 AC: 144116AN: 251344Hom.: 42896 AF XY: 0.583 AC XY: 79201AN XY: 135848
GnomAD4 exome AF: 0.618 AC: 902697AN: 1460160Hom.: 282765 Cov.: 49 AF XY: 0.619 AC XY: 449627AN XY: 726452
GnomAD4 genome AF: 0.606 AC: 92073AN: 152020Hom.: 28214 Cov.: 32 AF XY: 0.605 AC XY: 44982AN XY: 74316
ClinVar
Submissions by phenotype
not specified Benign:3
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Bietti crystalline corneoretinal dystrophy Benign:3
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:3
This variant is associated with the following publications: (PMID: 29083408, 18349091, 21232005, 20124536, 19278955) -
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Corneal dystrophy Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Retinal dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at