NM_007373.4(SHOC2):c.303T>C (p.Asn101=) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 23, 2019
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:: RCV000757762.13

Allele description [Variation Report for NM_007373.4(SHOC2):c.303T>C (p.Asn101=)]

NM_007373.4(SHOC2):c.303T>C (p.Asn101=)

Gene:

SHOC2:SHOC2 leucine rich repeat scaffold protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q25.2

Genomic location:

Preferred name:

NM_007373.4(SHOC2):c.303T>C (p.Asn101=)

HGVS:

NC_000010.11:g.110964661T>C
NG_028922.1:g.50119T>C
NM_001269039.3:c.303T>C
NM_001324336.2:c.303T>C
NM_001324337.2:c.303T>C
NM_007373.4:c.303T>CMANE SELECT
NP_001255968.1:p.Asn101=
NP_001311265.1:p.Asn101=
NP_001311266.1:p.Asn101=
NP_031399.2:p.Asn101=
NP_031399.2:p.Asn101=
LRG_753t1:c.303T>C
LRG_753:g.50119T>C
LRG_753p1:p.Asn101=
NC_000010.10:g.112724419T>C
NM_007373.3:c.303T>C
p.Asn101Asn

Links:

dbSNP: rs750568201

NCBI 1000 Genomes Browser:

rs750568201

Molecular consequence:

NM_001269039.3:c.303T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001324336.2:c.303T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001324337.2:c.303T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_007373.4:c.303T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000886108	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Mar 28, 2018)	germline	clinical testing	Citation Link,
SCV001855888	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Aug 23, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000886108

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Mar 28, 2018)

germline

clinical testing

Citation Link,

SCV001855888

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Aug 23, 2019)

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	not provided	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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000886108.1

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

Description

The c.303T>C p.Asn101Asn variant (rs750568201, ClinVar variant ID 260162), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with a Latino population frequency of 0.04% (identified on 14 out of 33,560 chromosomes). The variant affects a weakly conserved nucleotide, and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. Based on the available information, the c.303T>C variant is likely to be benign.

#	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 GeneDx, SCV001855888.1

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

#	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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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