chr10-68121394-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032578.4(MYPN):c.-1-44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,570,368 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 62 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 55 hom. )
Consequence
MYPN
NM_032578.4 intron
NM_032578.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.116
Genes affected
MYPN (HGNC:23246): (myopalladin) Striated muscle in vertebrates comprises large proteins which must be organized properly to contract efficiently. Z-lines in striated muscle are a sign of this organization, representing the ends of actin thin filaments, titin, nebulin or nebulette and accessory proteins required for structure and function. This gene encodes a protein which interacts with nebulin in skeletal muscle or nebulette in cardiac muscle and alpha-actinin. In addition, this gene product can interact with a protein with the I-band indicating it has a regulatory as well as structural function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 10-68121394-C-T is Benign according to our data. Variant chr10-68121394-C-T is described in ClinVar as [Benign]. Clinvar id is 1268670.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYPN | NM_032578.4 | c.-1-44C>T | intron_variant | ENST00000358913.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYPN | ENST00000358913.10 | c.-1-44C>T | intron_variant | 1 | NM_032578.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0169 AC: 2570AN: 152064Hom.: 62 Cov.: 32
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GnomAD3 exomes AF: 0.00455 AC: 1057AN: 232252Hom.: 20 AF XY: 0.00349 AC XY: 439AN XY: 125716
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GnomAD4 exome AF: 0.00179 AC: 2538AN: 1418186Hom.: 55 Cov.: 28 AF XY: 0.00160 AC XY: 1125AN XY: 705162
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GnomAD4 genome AF: 0.0169 AC: 2576AN: 152182Hom.: 62 Cov.: 32 AF XY: 0.0170 AC XY: 1264AN XY: 74406
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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 | Jun 14, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at