chr3-49012547-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018031.6(WDR6):c.1013C>T(p.Ser338Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,613,844 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.1013C>T | p.Ser338Leu | missense_variant | 2/6 | ENST00000608424.6 | |
WDR6 | NM_001320546.3 | c.935C>T | p.Ser312Leu | missense_variant | 2/6 | ||
WDR6 | NM_001320547.2 | c.860C>T | p.Ser287Leu | missense_variant | 2/6 | ||
WDR6 | XM_047447371.1 | c.1013C>T | p.Ser338Leu | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR6 | ENST00000608424.6 | c.1013C>T | p.Ser338Leu | missense_variant | 2/6 | 1 | NM_018031.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251290Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135836
GnomAD4 exome AF: 0.000150 AC: 220AN: 1461806Hom.: 0 Cov.: 34 AF XY: 0.000143 AC XY: 104AN XY: 727208
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.1103C>T (p.S368L) alteration is located in exon 2 (coding exon 2) of the WDR6 gene. This alteration results from a C to T substitution at nucleotide position 1103, causing the serine (S) at amino acid position 368 to be replaced by a leucine (L). 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