Analysis of copy number variations of WNT4 gene in a Chinese population with Müllerian anomalies

Table 2 CNV Interpretation Scoring Metric of ACMG

Patient no	Copy number status	Contain protein-coding elements (Score)^a	Haploinsufficient genes^b	Number of protein-coding RefSeq genes (Score)^c	Analysis of public databases and literature (Score)^d	Inheritance pattern for patient (Score)^e	Total score	Classification^f
1	Heterozygous deletion of WNT4	1A, Yes (0)	Skip	3A, 1 (0)	4E, reported phenotype is highly specific and relatively unique to WNT4. But the inheritance pattern of the variant is unknown (0.1)	5F, inheritance pattern is unknown (0)	0.1	VUS

^aGene type of WNT4: protein coding, Accession: NM_030761.5 (https://www.ncbi.nlm.nih.gov/)
^#The haploinsufficiency evaluation of WNT4 has not been established (https://dosage.clinicalgenome.org/), and WNT4 was predicted to be tolerated to haploinsufficiency (gnomAD version 2.1.1 and Haploinsufficiency Predictions Version 3)
^cWe targeted the WNT4 gene, so the number of protein-coding RefSeq genes is 1
^d,eThe blood of parents of the case is unavailable, so the inheritance pattern is unknown. But the patient has specific phenotype of MA and relatively unique to WNT4 in women. (ClinVar, http://www.ncbi.nlm.nih.gov/clinvar, OMIM, https://www.omim.org/)
^fPathogenic: total score ≥ 0.99 or more points; likely pathogenic: 0.90 < total score < 0.98; VUS, variant of uncertain significance: − 0.89 < total score < 0.89; likely benign: − 0.98 < total score < − 0.90; benign: total score ≤ − 0.99

ISSN: 1750-1172