X-71240948-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The ENST00000314425.9(ZMYM3):c.4081C>T(p.Leu1361=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000777 in 1,209,592 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., 9 hem., cov: 22)
Exomes 𝑓: 0.000043 ( 0 hom. 15 hem. )
Consequence
ZMYM3
ENST00000314425.9 synonymous
ENST00000314425.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.10
Genes affected
ZMYM3 (HGNC:13054): (zinc finger MYM-type containing 3) This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing multiprotein complexes that function through modifying chromatin structure to keep genes silent. A chromosomal translocation (X;13) involving this gene is associated with X-linked cognitive disability. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant X-71240948-G-A is Benign according to our data. Variant chrX-71240948-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3047138.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=3.1 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 9 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZMYM3 | NM_201599.3 | c.4081C>T | p.Leu1361= | synonymous_variant | 25/25 | ENST00000314425.9 | NP_963893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMYM3 | ENST00000314425.9 | c.4081C>T | p.Leu1361= | synonymous_variant | 25/25 | 1 | NM_201599.3 | ENSP00000322845 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000422 AC: 47AN: 111455Hom.: 0 Cov.: 22 AF XY: 0.000268 AC XY: 9AN XY: 33625
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GnomAD3 exomes AF: 0.000121 AC: 22AN: 182411Hom.: 0 AF XY: 0.000164 AC XY: 11AN XY: 67131
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GnomAD4 exome AF: 0.0000428 AC: 47AN: 1098086Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 15AN XY: 363448
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GnomAD4 genome AF: 0.000422 AC: 47AN: 111506Hom.: 0 Cov.: 22 AF XY: 0.000267 AC XY: 9AN XY: 33686
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ZMYM3-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at