1-109296778-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001010985.3(MYBPHL):c.730+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 1,614,012 control chromosomes in the GnomAD database, including 5,180 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001010985.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYBPHL | NM_001010985.3 | c.730+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000357155.2 | NP_001010985.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPHL | ENST00000357155.2 | c.730+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_001010985.3 | ENSP00000349678 | P1 | |||
MYBPHL | ENST00000477962.1 | n.150-1481G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0782 AC: 11894AN: 152074Hom.: 516 Cov.: 32
GnomAD3 exomes AF: 0.0636 AC: 15978AN: 251296Hom.: 638 AF XY: 0.0630 AC XY: 8554AN XY: 135804
GnomAD4 exome AF: 0.0756 AC: 110581AN: 1461820Hom.: 4664 Cov.: 57 AF XY: 0.0744 AC XY: 54140AN XY: 727220
GnomAD4 genome AF: 0.0782 AC: 11907AN: 152192Hom.: 516 Cov.: 32 AF XY: 0.0777 AC XY: 5783AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 28008009) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at