12-101595087-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000551300(MYBPC1):c.-452A>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000924 in 1,612,964 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000551300 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPC1 | ENST00000551300 | c.-452A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 32 | 1 | ENSP00000447116.1 | ||||
MYBPC1 | ENST00000361466.7 | c.17A>T | p.Lys6Met | missense_variant | Exon 1 of 32 | 1 | NM_002465.4 | ENSP00000354849.2 | ||
MYBPC1 | ENST00000551300 | c.-452A>T | 5_prime_UTR_variant | Exon 1 of 32 | 1 | ENSP00000447116.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000307 AC: 77AN: 251160Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135740
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1460644Hom.: 2 Cov.: 29 AF XY: 0.0000839 AC XY: 61AN XY: 726708
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74474
ClinVar
Submissions by phenotype
MYBPC1-related disorder Benign:1
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). -
Arthrogryposis, distal, type 1B Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at