chr7-99768360-A-G
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017460.6(CYP3A4):c.664T>C(p.Ser222Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 1,613,720 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017460.6 missense
Scores
Clinical Significance
Conservation
Publications
- vitamin D-dependent rickets, type 3Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP3A4 | ENST00000651514.1 | c.664T>C | p.Ser222Pro | missense_variant | Exon 7 of 13 | NM_017460.6 | ENSP00000498939.1 | |||
CYP3A4 | ENST00000336411.7 | c.664T>C | p.Ser222Pro | missense_variant | Exon 7 of 14 | 1 | ENSP00000337915.3 | |||
CYP3A4 | ENST00000652018.1 | c.517T>C | p.Ser173Pro | missense_variant | Exon 5 of 11 | ENSP00000498733.1 | ||||
CYP3A4 | ENST00000354593.6 | c.214T>C | p.Ser72Pro | missense_variant | Exon 2 of 8 | 5 | ENSP00000346607.2 |
Frequencies
GnomAD3 genomes AF: 0.000598 AC: 91AN: 152198Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000956 AC: 240AN: 251054 AF XY: 0.000855 show subpopulations
GnomAD4 exome AF: 0.000414 AC: 605AN: 1461404Hom.: 6 Cov.: 32 AF XY: 0.000424 AC XY: 308AN XY: 727028 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000597 AC: 91AN: 152316Hom.: 1 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74494 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at