rs575052082
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 8P and 10B. PVS1BP6_ModerateBS1BS2
The NM_001267822.1(ZMYND15):c.1852_1853delCT(p.Leu618fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,614,136 control chromosomes in the GnomAD database, including 50 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0025 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 46 hom. )
Consequence
ZMYND15
NM_001267822.1 frameshift
NM_001267822.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.963
Genes affected
ZMYND15 (HGNC:20997): (zinc finger MYND-type containing 15) This gene encodes a MYND-containing zinc-binding protein with a nuclear localization sequence. A similar gene in mice has been shown to act as a testis-specific transcriptional repressor by recruiting histone deacetylase enzymes to regulate spatiotemporal expression of many haploid genes. This protein may play an important role in spermatogenesis. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
BP6
Variant 17-4744855-CCT-C is Benign according to our data. Variant chr17-4744855-CCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 446037.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00251 (382/152278) while in subpopulation AMR AF= 0.0226 (345/15294). AF 95% confidence interval is 0.0206. There are 4 homozygotes in gnomad4. There are 216 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZMYND15 | NM_001136046.3 | c.1838-10_1838-9delCT | intron_variant | ENST00000433935.6 | NP_001129518.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMYND15 | ENST00000433935.6 | c.1838-10_1838-9delCT | intron_variant | 2 | NM_001136046.3 | ENSP00000391742.1 |
Frequencies
GnomAD3 genomes AF: 0.00249 AC: 379AN: 152160Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00653 AC: 1642AN: 251474Hom.: 37 AF XY: 0.00475 AC XY: 646AN XY: 135910
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GnomAD4 exome AF: 0.00137 AC: 2008AN: 1461858Hom.: 46 AF XY: 0.00112 AC XY: 813AN XY: 727236
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GnomAD4 genome AF: 0.00251 AC: 382AN: 152278Hom.: 4 Cov.: 32 AF XY: 0.00290 AC XY: 216AN XY: 74446
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 20, 2017 | - - |
Computational scores
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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 41
Find out detailed SpliceAI scores and Pangolin per-transcript scores at