3-50342981-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015896.4(ZMYND10):c.637C>A(p.His213Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H213Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_015896.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND10 | NM_015896.4 | c.637C>A | p.His213Asn | missense_variant | 7/12 | ENST00000231749.8 | |
ZMYND10 | XM_005265216.4 | c.400C>A | p.His134Asn | missense_variant | 6/11 | ||
ZMYND10 | NM_001308379.2 | c.599+137C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND10 | ENST00000231749.8 | c.637C>A | p.His213Asn | missense_variant | 7/12 | 1 | NM_015896.4 | P1 | |
ZMYND10-AS1 | ENST00000440013.1 | n.123+1753G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727224
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 05, 2018 | This sequence change replaces histidine with asparagine at codon 213 of the ZMYND10 protein (p.His213Asn). The histidine residue is highly conserved and there is a small physicochemical difference between histidine and asparagine. This variant is present in population databases (rs199711270, ExAC 0.009%). This variant has not been reported in the literature in individuals with ZMYND10-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at