16-81290555-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_017429.3(BCO1):c.1622G>A(p.Cys541Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00654 in 1,613,678 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017429.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCO1 | NM_017429.3 | c.1622G>A | p.Cys541Tyr | missense_variant | 11/11 | ENST00000258168.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCO1 | ENST00000258168.7 | c.1622G>A | p.Cys541Tyr | missense_variant | 11/11 | 1 | NM_017429.3 | P1 | |
BCO1 | ENST00000563804.5 | c.*1246G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00623 AC: 948AN: 152132Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00715 AC: 1795AN: 250954Hom.: 18 AF XY: 0.00775 AC XY: 1052AN XY: 135676
GnomAD4 exome AF: 0.00657 AC: 9601AN: 1461428Hom.: 57 Cov.: 31 AF XY: 0.00692 AC XY: 5034AN XY: 727056
GnomAD4 genome AF: 0.00624 AC: 950AN: 152250Hom.: 6 Cov.: 33 AF XY: 0.00654 AC XY: 487AN XY: 74446
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 13, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at