Submissions for variant NM_017654.4(SAMD9):c.4733T>C (p.Ile1578Thr)

gnomAD frequency: 0.00655  dbSNP: rs144380633

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000948779	SCV001095001	benign	not provided	2024-01-31	criteria provided, single submitter	clinical testing
GeneDx	RCV000948779	SCV001940106	benign	not provided	2020-02-19	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV001818946	SCV002069917	benign	not specified	2017-09-20	criteria provided, single submitter	clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV003227878	SCV003924159	likely benign	Normophosphatemic familial tumoral calcinosis; MIRAGE syndrome; Monosomy 7 myelodysplasia and leukemia syndrome 2	2021-03-30	criteria provided, single submitter	clinical testing	SAMD9 NM_017654.3 exon 3 p.Ile1578Thr (c.4733T>C): This variant has not been reported in the literature but is present in 0.09% (643/67964) of European alleles including 2 homozygotes in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/7-93101365-A-G?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:769723). This variant amino acid Threonine (Thr) is present in 3 species (Pig, Tasmanian Devil, Opossum) and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant suggests that this variant does not cause disease, but requires further evidence. Therefore this variant is classified as likely benign.
CeGaT Center for Human Genetics Tuebingen	RCV000948779	SCV004164310	likely benign	not provided	2024-04-01	criteria provided, single submitter	clinical testing	SAMD9: BP4, BS2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000948779	SCV004563100	likely benign	not provided	2023-11-16	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV000948779	SCV005268679	benign	not provided		criteria provided, single submitter	not provided
PreventionGenetics, part of Exact Sciences	RCV004553389	SCV004748712	benign	SAMD9-related disorder	2019-03-12	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).