chr10-120906788-T-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_018117.12(WDR11):āc.3450T>Gā(p.Phe1150Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00047 in 1,614,192 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018117.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR11 | ENST00000263461.11 | c.3450T>G | p.Phe1150Leu | missense_variant | Exon 28 of 29 | 1 | NM_018117.12 | ENSP00000263461.5 | ||
WDR11 | ENST00000497136.6 | n.*2723T>G | non_coding_transcript_exon_variant | Exon 25 of 26 | 1 | ENSP00000474595.1 | ||||
WDR11 | ENST00000605543.5 | n.*1969T>G | non_coding_transcript_exon_variant | Exon 21 of 22 | 2 | ENSP00000475076.1 | ||||
WDR11 | ENST00000497136.6 | n.*2723T>G | 3_prime_UTR_variant | Exon 25 of 26 | 1 | ENSP00000474595.1 | ||||
WDR11 | ENST00000605543.5 | n.*1969T>G | 3_prime_UTR_variant | Exon 21 of 22 | 2 | ENSP00000475076.1 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000700 AC: 176AN: 251452Hom.: 0 AF XY: 0.000729 AC XY: 99AN XY: 135892
GnomAD4 exome AF: 0.000484 AC: 708AN: 1461852Hom.: 1 Cov.: 32 AF XY: 0.000503 AC XY: 366AN XY: 727220
GnomAD4 genome AF: 0.000335 AC: 51AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:3Other:1
See Variant Classification Assertion Criteria. -
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WDR11: PP3, PS3:Supporting, BS1, BS2 -
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Hypogonadotropic hypogonadism 14 with or without anosmia Pathogenic:1Uncertain:1Benign:1
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See cases Uncertain:1
ACMG categories: PP2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at