rs139849511
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001010985.3(MYBPHL):c.763C>T(p.Arg255*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000921 in 1,614,156 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001010985.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPHL | ENST00000357155.2 | c.763C>T | p.Arg255* | stop_gained | Exon 6 of 9 | 1 | NM_001010985.3 | ENSP00000349678.1 | ||
MYBPHL | ENST00000477962.1 | n.150-1041C>T | intron_variant | Intron 1 of 3 | 1 | |||||
MYBPHL | ENST00000489706.5 | n.16C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000979 AC: 149AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00128 AC: 321AN: 251480Hom.: 0 AF XY: 0.00125 AC XY: 170AN XY: 135914
GnomAD4 exome AF: 0.000915 AC: 1337AN: 1461882Hom.: 2 Cov.: 36 AF XY: 0.000945 AC XY: 687AN XY: 727242
GnomAD4 genome AF: 0.000978 AC: 149AN: 152274Hom.: 0 Cov.: 31 AF XY: 0.000779 AC XY: 58AN XY: 74464
ClinVar
Submissions by phenotype
not provided Uncertain:2
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Brugada syndrome Uncertain:1
Heterozygous variant NM_001010985:c.763C>T (p.Arg255*) in the MYBPHL gene was found on WES data in male proband (24 y.o., Caucasian) with Brugada-like ECG. Two additional rare candidate variants: NM_004415:c.5512C>T (p.Arg1838Cys) in the DSP gene (Class III of pathogenicity) and NM_001148:c.8899C>G (p.Pro2967Ala) in the ANK2 gene (Class III of pathogenicity) - were found in this proband. This variant is in The Genome Aggregation Database (gnomAD) v2.1.1 with total MAF 0.001404 (Date of access 06-03-2023). Clinvar contains an entry for this variant (Variation ID: 994289). This variant has been reported in one study (PMID: 28778945) showing that the R255X is subject to NMD, a direct study of MYBPHL (PMID: 35533732) provides evidence of atrioventricular dysfunction following loss of Mybphl. Most in silico predictors show benign result of the protein change (varsome.com). In accordance with ACMG(2015) criteria this variant is classified as Variant of Uncertain Significance (VUS) with following criteria selected: PS3, BS1. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at