chr8-58491697-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000780.4(CYP7A1):c.1293G>T(p.Lys431Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000861 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K431R) has been classified as Likely benign.
Frequency
Consequence
NM_000780.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP7A1 | NM_000780.4 | c.1293G>T | p.Lys431Asn | missense_variant | 6/6 | ENST00000301645.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP7A1 | ENST00000301645.4 | c.1293G>T | p.Lys431Asn | missense_variant | 6/6 | 1 | NM_000780.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251108Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135794
GnomAD4 exome AF: 0.0000903 AC: 132AN: 1461452Hom.: 0 Cov.: 30 AF XY: 0.0000784 AC XY: 57AN XY: 727056
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.1293G>T (p.K431N) alteration is located in exon 6 (coding exon 6) of the CYP7A1 gene. This alteration results from a G to T substitution at nucleotide position 1293, causing the lysine (K) at amino acid position 431 to be replaced by an asparagine (N). 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