1-109296811-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001010985.3(MYBPHL):āc.702T>Cā(p.Thr234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 1,614,102 control chromosomes in the GnomAD database, including 788,713 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.93 ( 67126 hom., cov: 31)
Exomes š: 0.99 ( 721587 hom. )
Consequence
MYBPHL
NM_001010985.3 synonymous
NM_001010985.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.813
Genes affected
MYBPHL (HGNC:30434): (myosin binding protein H like) This gene encodes a protein with two immunoglobulin superfamily domains and a fibronectin 3 domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 1-109296811-A-G is Benign according to our data. Variant chr1-109296811-A-G is described in ClinVar as [Benign]. Clinvar id is 1265643.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.813 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYBPHL | NM_001010985.3 | c.702T>C | p.Thr234= | synonymous_variant | 5/9 | ENST00000357155.2 | NP_001010985.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPHL | ENST00000357155.2 | c.702T>C | p.Thr234= | synonymous_variant | 5/9 | 1 | NM_001010985.3 | ENSP00000349678 | P1 | |
MYBPHL | ENST00000477962.1 | n.150-1514T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.934 AC: 142064AN: 152090Hom.: 67089 Cov.: 31
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GnomAD3 exomes AF: 0.982 AC: 246979AN: 251482Hom.: 121715 AF XY: 0.987 AC XY: 134112AN XY: 135914
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GnomAD4 exome AF: 0.993 AC: 1451548AN: 1461894Hom.: 721587 Cov.: 67 AF XY: 0.994 AC XY: 722753AN XY: 727248
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GnomAD4 genome AF: 0.934 AC: 142161AN: 152208Hom.: 67126 Cov.: 31 AF XY: 0.936 AC XY: 69648AN XY: 74422
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at