chr7-141709058-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001105558.1(WEE2):c.300C>T(p.Ser100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,614,100 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 12 hom. )
Consequence
WEE2
NM_001105558.1 synonymous
NM_001105558.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
WEE2 (HGNC:19684): (WEE2 oocyte meiosis inhibiting kinase) Predicted to enable protein tyrosine kinase activity. Predicted to be involved in several processes, including female pronucleus assembly; negative regulation of oocyte maturation; and regulation of meiosis I. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 7-141709058-C-T is Benign according to our data. Variant chr7-141709058-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3041408.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.21 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000276 (42/152270) while in subpopulation SAS AF= 0.00872 (42/4818). AF 95% confidence interval is 0.00663. There are 1 homozygotes in gnomad4. There are 32 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WEE2 | NM_001105558.1 | c.300C>T | p.Ser100= | synonymous_variant | 1/12 | ENST00000397541.6 | |
WEE2-AS1 | NR_015392.1 | n.843-3301G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WEE2 | ENST00000397541.6 | c.300C>T | p.Ser100= | synonymous_variant | 1/12 | 1 | NM_001105558.1 | P1 | |
WEE2-AS1 | ENST00000665340.1 | n.618-3301G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152152Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000779 AC: 194AN: 248986Hom.: 4 AF XY: 0.00109 AC XY: 147AN XY: 135076
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GnomAD4 exome AF: 0.000393 AC: 575AN: 1461830Hom.: 12 Cov.: 31 AF XY: 0.000591 AC XY: 430AN XY: 727202
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
WEE2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 05, 2019 | 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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at