10-28533659-G-GGGCGGC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_016628.5(WAC):c.41+45_41+50dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,540,618 control chromosomes in the GnomAD database, including 55 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 27 hom. )
Consequence
WAC
NM_016628.5 intron
NM_016628.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.40
Genes affected
WAC (HGNC:17327): (WW domain containing adaptor with coiled-coil) The protein encoded by this gene contains a WW domain, which is a protein module found in a wide range of signaling proteins. This domain mediates protein-protein interactions and binds proteins containing short linear peptide motifs that are proline-rich or contain at least one proline. This gene product shares 94% sequence identity with the WAC protein in mouse, however, its exact function is not known. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 10-28533659-G-GGGCGGC is Benign according to our data. Variant chr10-28533659-G-GGGCGGC is described in ClinVar as [Likely_benign]. Clinvar id is 1219860.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0103 (1560/150948) while in subpopulation AFR AF= 0.0358 (1475/41216). AF 95% confidence interval is 0.0343. There are 28 homozygotes in gnomad4. There are 773 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1559 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WAC | NM_016628.5 | c.41+45_41+50dup | intron_variant | ENST00000354911.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WAC | ENST00000354911.9 | c.41+45_41+50dup | intron_variant | 1 | NM_016628.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1559AN: 150838Hom.: 28 Cov.: 32
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GnomAD3 exomes AF: 0.00240 AC: 367AN: 152914Hom.: 19 AF XY: 0.00219 AC XY: 183AN XY: 83516
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GnomAD4 exome AF: 0.00100 AC: 1391AN: 1389670Hom.: 27 Cov.: 29 AF XY: 0.000888 AC XY: 610AN XY: 686906
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GnomAD4 genome ? AF: 0.0103 AC: 1560AN: 150948Hom.: 28 Cov.: 32 AF XY: 0.0105 AC XY: 773AN XY: 73746
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 19, 2020 | - - |
Computational scores
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Name
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at