Submissions for variant NM_006118.4(HAX1):c.207A>T (p.Pro69=)

gnomAD frequency: 0.00228  dbSNP: rs142150013

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000532229	SCV000348479	likely benign	Kostmann syndrome	2018-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genetic Services Laboratory, University of Chicago	RCV000502834	SCV000595091	benign	not specified	2021-04-21	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000532229	SCV000657555	benign	Kostmann syndrome	2025-01-30	criteria provided, single submitter	clinical testing
GeneDx	RCV001702413	SCV001942785	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001702413	SCV003916501	likely benign	not provided	2023-02-01	criteria provided, single submitter	clinical testing	HAX1: BP4, BP7
Breakthrough Genomics, Breakthrough Genomics	RCV001702413	SCV005262209	likely benign	not provided		criteria provided, single submitter	not provided
Ambry Genetics	RCV004975416	SCV005596126	likely benign	Inborn genetic diseases	2024-10-02	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc.	RCV000532229	SCV001461736	benign	Kostmann syndrome	2020-09-16	no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV001702413	SCV001932102	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001702413	SCV001964607	likely benign	not provided		no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003930202	SCV004741977	benign	HAX1-related disorder	2021-08-04	no assertion criteria provided	clinical testing	This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).