NM_001385641.1(SAMD11):c.2084AGG[1] (p.Glu696del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 3, 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:: RCV001213543.8

Allele description [Variation Report for NM_001385641.1(SAMD11):c.2084AGG[1] (p.Glu696del)]

NM_001385641.1(SAMD11):c.2084AGG[1] (p.Glu696del)

Genes:

LOC129929063:ATAC-STARR-seq lymphoblastoid active region 4 [Gene]
SAMD11:sterile alpha motif domain containing 11 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

1p36.33

Genomic location:

Preferred name:

NM_001385641.1(SAMD11):c.2084AGG[1] (p.Glu696del)

HGVS:

NC_000001.11:g.943283AGG[1]
NM_001385640.1:c.2087AGG[1]
NM_001385641.1:c.2084AGG[1]MANE SELECT
NM_152486.4:c.1595AGG[1]
NM_152486.4:c.1595AGG[1]
NP_001372569.1:p.Glu697del
NP_001372570.1:p.Glu696del
NP_689699.3:p.Glu533del
NC_000001.10:g.878661_878663del
NC_000001.10:g.878663AGG[1]
NM_152486.2:c.1598_1600del

Protein change:

E533del

Links:

dbSNP: rs779142409

NCBI 1000 Genomes Browser:

rs779142409

Molecular consequence:

NM_001385640.1:c.2087AGG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001385641.1:c.2084AGG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_152486.4:c.1595AGG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV001385178	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 3, 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

SCV001385178

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 3, 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, SCV001385178.5

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 943368). This variant has not been reported in the literature in individuals affected with SAMD11-related conditions. This variant is present in population databases (rs779142409, gnomAD 0.005%). This variant, c.1598_1600del, results in the deletion of 1 amino acid(s) of the SAMD11 protein (p.Glu533del), but otherwise preserves the integrity of the reading frame.

#	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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