chr10-209870-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001370100.5(ZMYND11):c.117-19G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000203 in 1,574,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
ZMYND11
NM_001370100.5 intron
NM_001370100.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.32
Genes affected
ZMYND11 (HGNC:16966): (zinc finger MYND-type containing 11) The protein encoded by this gene was first identified by its ability to bind the adenovirus E1A protein. The protein localizes to the nucleus. It functions as a transcriptional repressor, and expression of E1A inhibits this repression. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 10-209870-G-T is Benign according to our data. Variant chr10-209870-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1977357.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000395 (6/151944) while in subpopulation AMR AF= 0.000262 (4/15252). AF 95% confidence interval is 0.0000889. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND11 | NM_001370100.5 | c.117-19G>T | intron_variant | ENST00000381604.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND11 | ENST00000381604.9 | c.117-19G>T | intron_variant | 5 | NM_001370100.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151944Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000261 AC: 6AN: 229578Hom.: 0 AF XY: 0.0000241 AC XY: 3AN XY: 124286
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GnomAD4 exome AF: 0.0000183 AC: 26AN: 1422346Hom.: 0 Cov.: 30 AF XY: 0.0000142 AC XY: 10AN XY: 703652
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 151944Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74168
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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 | Invitae | Dec 09, 2023 | - - |
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