3-50343153-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_015896.4(ZMYND10):c.564C>T(p.Leu188=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,124 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 (★). Synonymous variant affecting the same amino acid position (i.e. L188L) has been classified as Likely benign.
Frequency
Consequence
NM_015896.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND10 | NM_015896.4 | c.564C>T | p.Leu188= | synonymous_variant | 6/12 | ENST00000231749.8 | |
ZMYND10 | NM_001308379.2 | c.564C>T | p.Leu188= | synonymous_variant | 6/11 | ||
ZMYND10 | XM_005265216.4 | c.327C>T | p.Leu109= | synonymous_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND10 | ENST00000231749.8 | c.564C>T | p.Leu188= | synonymous_variant | 6/12 | 1 | NM_015896.4 | P1 | |
ZMYND10-AS1 | ENST00000440013.1 | n.123+1925G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251414Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135890
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.0000330 AC XY: 24AN XY: 727246
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 19, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at