rs201896308
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015896.4(ZMYND10):c.478G>A(p.Gly160Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000405 in 1,612,846 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. G160G) has been classified as Benign.
Frequency
Consequence
NM_015896.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND10 | NM_015896.4 | c.478G>A | p.Gly160Arg | missense_variant | 5/12 | ENST00000231749.8 | |
ZMYND10 | NM_001308379.2 | c.478G>A | p.Gly160Arg | missense_variant | 5/11 | ||
ZMYND10 | XM_005265216.4 | c.241G>A | p.Gly81Arg | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND10 | ENST00000231749.8 | c.478G>A | p.Gly160Arg | missense_variant | 5/12 | 1 | NM_015896.4 | P1 | |
ZMYND10-AS1 | ENST00000440013.1 | n.123+2111C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000604 AC: 92AN: 152232Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00109 AC: 271AN: 249744Hom.: 6 AF XY: 0.000940 AC XY: 127AN XY: 135046
GnomAD4 exome AF: 0.000385 AC: 562AN: 1460496Hom.: 16 Cov.: 33 AF XY: 0.000326 AC XY: 237AN XY: 726514
GnomAD4 genome ? AF: 0.000604 AC: 92AN: 152350Hom.: 3 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74498
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2022 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at