chr1-46814237-C-G
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001099772.2(CYP4B1):āc.804C>Gā(p.Ala268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,614,020 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 32)
Exomes š: 0.000068 ( 2 hom. )
Consequence
CYP4B1
NM_001099772.2 synonymous
NM_001099772.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.940
Genes affected
CYP4B1 (HGNC:2644): (cytochrome P450 family 4 subfamily B member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum. In rodents, the homologous protein has been shown to metabolize certain carcinogens; however, the specific function of the human protein has not been determined. Multiple transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 1-46814237-C-G is Benign according to our data. Variant chr1-46814237-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 740563.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.94 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4B1 | NM_001099772.2 | c.804C>G | p.Ala268= | synonymous_variant | 7/12 | ENST00000371923.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4B1 | ENST00000371923.9 | c.804C>G | p.Ala268= | synonymous_variant | 7/12 | 1 | NM_001099772.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251058Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135708
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GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461868Hom.: 2 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727240
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74334
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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