3-49012769-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018031.6(WDR6):c.1235A>G(p.Asn412Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018031.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR6 | NM_018031.6 | c.1235A>G | p.Asn412Ser | missense_variant | 2/6 | ENST00000608424.6 | |
WDR6 | NM_001320546.3 | c.1157A>G | p.Asn386Ser | missense_variant | 2/6 | ||
WDR6 | NM_001320547.2 | c.1082A>G | p.Asn361Ser | missense_variant | 2/6 | ||
WDR6 | XM_047447371.1 | c.1235A>G | p.Asn412Ser | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR6 | ENST00000608424.6 | c.1235A>G | p.Asn412Ser | missense_variant | 2/6 | 1 | NM_018031.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251372Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135870
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1461828Hom.: 0 Cov.: 34 AF XY: 0.0000688 AC XY: 50AN XY: 727216
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1325A>G (p.N442S) alteration is located in exon 2 (coding exon 2) of the WDR6 gene. This alteration results from a A to G substitution at nucleotide position 1325, causing the asparagine (N) at amino acid position 442 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at