1-34988017-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_007167.4(ZMYM6):āc.3065T>Cā(p.Leu1022Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000069 in 1,551,378 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 (no stars).
Frequency
Consequence
NM_007167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMYM6 | ENST00000357182.9 | c.3065T>C | p.Leu1022Ser | missense_variant | Exon 16 of 16 | 1 | NM_007167.4 | ENSP00000349708.4 | ||
ZMYM6 | ENST00000493328.5 | n.4389T>C | non_coding_transcript_exon_variant | Exon 15 of 15 | 1 | |||||
ENSG00000271741 | ENST00000487874.1 | n.2147-4070T>C | intron_variant | Intron 15 of 16 | 5 | ENSP00000421752.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000561 AC: 85AN: 151630Hom.: 0 AF XY: 0.000435 AC XY: 35AN XY: 80454
GnomAD4 exome AF: 0.0000700 AC: 98AN: 1399084Hom.: 0 Cov.: 31 AF XY: 0.0000623 AC XY: 43AN XY: 690002
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74472
ClinVar
Submissions by phenotype
ZMYM6-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at