chr10-180148-A-G
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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.116+20A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 1,585,826 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00063 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00041 ( 4 hom. )
Consequence
ZMYND11
NM_001370100.5 intron
NM_001370100.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.52
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=-0.81).
BP6
Variant 10-180148-A-G is Benign according to our data. Variant chr10-180148-A-G is described in ClinVar as [Benign]. Clinvar id is 1971355.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00063 (96/152326) while in subpopulation EAS AF= 0.0166 (86/5192). AF 95% confidence interval is 0.0137. There are 1 homozygotes in gnomad4. There are 56 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 96 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND11 | NM_001370100.5 | c.116+20A>G | intron_variant | ENST00000381604.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND11 | ENST00000381604.9 | c.116+20A>G | intron_variant | 5 | NM_001370100.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000637 AC: 97AN: 152208Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00144 AC: 350AN: 243114Hom.: 4 AF XY: 0.00145 AC XY: 191AN XY: 131906
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GnomAD4 exome AF: 0.000409 AC: 587AN: 1433500Hom.: 4 Cov.: 24 AF XY: 0.000447 AC XY: 319AN XY: 714414
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GnomAD4 genome AF: 0.000630 AC: 96AN: 152326Hom.: 1 Cov.: 33 AF XY: 0.000752 AC XY: 56AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
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