rs768442659
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004820.5(CYP7B1):āc.987A>Gā(p.Thr329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,498 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. T329T) has been classified as Likely benign.
Frequency
Consequence
NM_004820.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP7B1 | NM_004820.5 | c.987A>G | p.Thr329= | synonymous_variant | 4/6 | ENST00000310193.4 | |
CYP7B1 | NM_001324112.2 | c.987A>G | p.Thr329= | synonymous_variant | 4/7 | ||
CYP7B1 | XM_017014002.2 | c.1053A>G | p.Thr351= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP7B1 | ENST00000310193.4 | c.987A>G | p.Thr329= | synonymous_variant | 4/6 | 1 | NM_004820.5 | P1 | |
CYP7B1 | ENST00000523954.1 | n.261A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251238Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135762
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461498Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727052
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at