chr8-58491581-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000780.4(CYP7A1):c.1409T>C(p.Ile470Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000527 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I470I) has been classified as Likely benign.
Frequency
Consequence
NM_000780.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP7A1 | NM_000780.4 | c.1409T>C | p.Ile470Thr | missense_variant | 6/6 | ENST00000301645.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP7A1 | ENST00000301645.4 | c.1409T>C | p.Ile470Thr | missense_variant | 6/6 | 1 | NM_000780.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000267 AC: 67AN: 251406Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135910
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727236
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 24, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 16, 2021 | - - |
CYP7A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 05, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at