20-41202259-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001384317.1(ZHX3):āc.2658A>Gā(p.Lys886Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000704 in 1,614,092 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001384317.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZHX3 | NM_001384317.1 | c.2658A>G | p.Lys886Lys | synonymous_variant | Exon 3 of 4 | ENST00000683867.1 | NP_001371246.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00346 AC: 527AN: 152096Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000935 AC: 235AN: 251324Hom.: 3 AF XY: 0.000685 AC XY: 93AN XY: 135816
GnomAD4 exome AF: 0.000417 AC: 609AN: 1461878Hom.: 7 Cov.: 31 AF XY: 0.000320 AC XY: 233AN XY: 727240
GnomAD4 genome AF: 0.00347 AC: 528AN: 152214Hom.: 2 Cov.: 32 AF XY: 0.00348 AC XY: 259AN XY: 74426
ClinVar
Submissions by phenotype
ZHX3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at