NM_005343.4(HRAS):c.369C>T (p.Arg123=) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Sep 20, 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:: RCV000588992.16

Allele description [Variation Report for NM_005343.4(HRAS):c.369C>T (p.Arg123=)]

NM_005343.4(HRAS):c.369C>T (p.Arg123=)

Genes:

HRAS:HRas proto-oncogene, GTPase [Gene - OMIM - HGNC]
LRRC56:leucine rich repeat containing 56 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.5

Genomic location:

Preferred name:

NM_005343.4(HRAS):c.369C>T (p.Arg123=)

Other names:

NM_005343.3(HRAS):c.369C>T

HGVS:

NC_000011.10:g.533534G>A
NG_007666.1:g.7017C>T
NM_001130442.3:c.369C>T
NM_001318054.2:c.50C>T
NM_005343.4:c.369C>TMANE SELECT
NM_176795.5:c.369C>T
NP_001123914.1:p.Arg123=
NP_001304983.1:p.Ala17Val
NP_005334.1:p.Arg123=
NP_789765.1:p.Arg123=
LRG_506t1:c.369C>T
LRG_506:g.7017C>T
LRG_506p1:p.Arg123=
NC_000011.9:g.533534G>A
NM_005343.2:c.369C>T
NM_005343.3:c.369C>T
p.Arg123Arg

Protein change:

A17V

Links:

dbSNP: rs200945755

NCBI 1000 Genomes Browser:

rs200945755

Molecular consequence:

NM_001318054.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001130442.3:c.369C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005343.4:c.369C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_176795.5:c.369C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698556	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jan 23, 2017)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV004134984	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Sep 1, 2023)	germline	clinical testing	Citation Link,
SCV004564966	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Sep 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698556

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jan 23, 2017)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV004134984

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Likely benign
(Sep 1, 2023)

germline

clinical testing

Citation Link,

SCV004564966

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Sep 20, 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	1	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698556.1

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

Description

Variant summary: The HRAS c.369C>T (p.Arg123Arg) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. It is 81 nucleotides upstream from exon-intron boundary. 2/5 splice prediction tools predict a creation of cryptic splice donor site. ESE finder predicts that this variant may affect binding of ESE site(s). However, these predictions have yet to be confirmed by functional studies. This variant was found in 13/120964 control chromosomes, exclusively observed in the East Asian subpopulation at a frequency of 0.001505 (13/8638). This frequency is about 602 times the estimated maximal expected allele frequency of a pathogenic HRAS variant (0.0000025), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. In addition, one clinical diagnostic laboratory has classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories. Taken together, this variant is classified as 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 CeGaT Center for Human Genetics Tuebingen, SCV004134984.12

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

Description

HRAS: BP4, BP7

#	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		1	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004564966.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 22, 2025

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