NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Dec 14, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002515744.16

Allele description [Variation Report for NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)]

NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)

Genes:

LOC130004821:ATAC-STARR-seq lymphoblastoid silent region 2865 [Gene]
NANOS1:nanos C2HC-type zinc finger 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q26.11

Genomic location:

Preferred name:

NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)

Other names:

S78del

HGVS:

NC_000010.11:g.119030032CTC[3]
NG_050764.1:g.5317CTC[3]
NM_199461.3:c.240_242delCTC
NM_199461.4:c.231CTC[3]MANE SELECT
NP_955631.1:p.Ser83del
NC_000010.10:g.120789543_120789545del
NC_000010.10:g.120789544CTC[3]
NM_199461.2:c.240_242delCTC

Protein change:

S83del; SER78DEL

Links:

OMIM: 608226.0001; dbSNP: rs587777031

NCBI 1000 Genomes Browser:

rs587777031

Molecular consequence:

NM_199461.4:c.231CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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LPGAT1 [Aptenodytes forsteri]
LPGAT1 [Aptenodytes forsteri]
Gene ID:103899175

Gene
dpagt1 [Siniperca chuatsi]
dpagt1 [Siniperca chuatsi]
Gene ID:122888868

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003251459	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Dec 14, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003916645	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Dec 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003251459

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Dec 14, 2023)

germline

clinical testing

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

SCV003916645

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Dec 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
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, SCV003251459.2

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV003916645.13

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

NANOS1: PM4:Supporting, BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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