chr10-134900-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000509513.6(ZMYND11):c.-20+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 151,344 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000509513.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND11 | NM_001370098.2 | c.-323C>A | 5_prime_UTR_variant | 1/15 | |||
ZMYND11 | NM_001370107.2 | c.-323C>A | 5_prime_UTR_variant | 1/14 | |||
ZMYND11 | NM_001370113.2 | c.-323C>A | 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND11 | ENST00000397962.8 | c.-20+114C>A | intron_variant | 1 | P4 | ||||
ZMYND11 | ENST00000509513.6 | c.-20+8C>A | splice_region_variant, intron_variant | 1 | |||||
ZMYND11 | ENST00000439456.5 | c.-20+114C>A | intron_variant | 4 | |||||
ZMYND11 | ENST00000704295.1 | c.-20+4565C>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151344Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 0
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151344Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73870
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 30 Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Institute of Human Genetics, University Hospital of Duesseldorf | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at