NM_152703.5(SAMD9L):c.4708G>T (p.Gly1570Ter) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001929873.4

Allele description [Variation Report for NM_152703.5(SAMD9L):c.4708G>T (p.Gly1570Ter)]

NM_152703.5(SAMD9L):c.4708G>T (p.Gly1570Ter)

Gene:

SAMD9L:sterile alpha motif domain containing 9 like [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.2

Genomic location:

Preferred name:

NM_152703.5(SAMD9L):c.4708G>T (p.Gly1570Ter)

HGVS:

NC_000007.14:g.93131264C>A
NG_053186.1:g.22138G>T
NM_001303496.3:c.4708G>T
NM_001303497.3:c.4708G>T
NM_001303498.3:c.4708G>T
NM_001303500.3:c.4708G>T
NM_001350082.2:c.4708G>T
NM_001350083.2:c.4708G>T
NM_001350084.2:c.4708G>T
NM_001350085.2:c.4708G>T
NM_152703.5:c.4708G>TMANE SELECT
NP_001290425.1:p.Gly1570Ter
NP_001290426.1:p.Gly1570Ter
NP_001290427.1:p.Gly1570Ter
NP_001290429.1:p.Gly1570Ter
NP_001337011.1:p.Gly1570Ter
NP_001337012.1:p.Gly1570Ter
NP_001337013.1:p.Gly1570Ter
NP_001337014.1:p.Gly1570Ter
NP_689916.2:p.Gly1570Ter
NC_000007.13:g.92760577C>A

Protein change:

G1570*

Links:

dbSNP: rs2116467146

NCBI 1000 Genomes Browser:

rs2116467146

Molecular consequence:

NM_001303496.3:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001303497.3:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001303498.3:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001303500.3:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350082.2:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350083.2:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350084.2:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001350085.2:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_152703.5:c.4708G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002133150	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002133150

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002133150.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change creates a premature translational stop signal (p.Gly1570*) in the SAMD9L gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 15 amino acid(s) of the SAMD9L protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SAMD9L-related conditions. ClinVar contains an entry for this variant (Variation ID: 1365581). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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