NM_000765.5:c.1328T>C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000765.5(CYP3A7):c.1328T>C(p.Ile443Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000765.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP3A7 | ENST00000336374.4 | c.1328T>C | p.Ile443Thr | missense_variant | Exon 12 of 13 | 1 | NM_000765.5 | ENSP00000337450.2 | ||
CYP3A7-CYP3A51P | ENST00000620220.6 | c.1328T>C | p.Ile443Thr | missense_variant | Exon 12 of 13 | 1 | ENSP00000479282.3 | |||
CYP3A7-CYP3A51P | ENST00000611620.4 | c.1328T>C | p.Ile443Thr | missense_variant | Exon 12 of 15 | 5 | ENSP00000480571.1 | |||
CYP3A7 | ENST00000477357.5 | n.1667T>C | non_coding_transcript_exon_variant | Exon 9 of 10 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251342Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135832
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727158
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1328T>C (p.I443T) alteration is located in exon 12 (coding exon 12) of the CYP3A7 gene. This alteration results from a T to C substitution at nucleotide position 1328, causing the isoleucine (I) at amino acid position 443 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at