NM_003001.5(SDHC):c.354T>C (p.Phe118=) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jan 1, 2024
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:: RCV000589493.24

Allele description [Variation Report for NM_003001.5(SDHC):c.354T>C (p.Phe118=)]

NM_003001.5(SDHC):c.354T>C (p.Phe118=)

Gene:

SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_003001.5(SDHC):c.354T>C (p.Phe118=)

HGVS:

NC_000001.11:g.161356789T>C
NG_012767.1:g.47414T>C
NM_001035511.3:c.242-5540T>C
NM_001035512.3:c.252T>C
NM_001035513.3:c.195T>C
NM_001278172.3:c.140-5540T>C
NM_001407115.1:c.474T>C
NM_001407116.1:c.297T>C
NM_001407117.1:c.291T>C
NM_001407118.1:c.246T>C
NM_001407119.1:c.243T>C
NM_001407120.1:c.243T>C
NM_001407121.1:c.185-5540T>C
NM_003001.5:c.354T>CMANE SELECT
NP_001030589.1:p.Phe84=
NP_001030590.1:p.Phe65=
NP_001394044.1:p.Phe158=
NP_001394045.1:p.Phe99=
NP_001394046.1:p.Phe97=
NP_001394047.1:p.Phe82=
NP_001394048.1:p.Phe81=
NP_001394049.1:p.Phe81=
NP_002992.1:p.Phe118=
NP_002992.1:p.Phe118=
LRG_317t1:c.354T>C
LRG_317:g.47414T>C
LRG_317p1:p.Phe118=
NC_000001.10:g.161326579T>C
NM_003001.3:c.354T>C
NR_103459.3:n.406T>C
p.F118F
p.Phe118Phe

Links:

dbSNP: rs61733156

NCBI 1000 Genomes Browser:

rs61733156

Molecular consequence:

NM_001035511.3:c.242-5540T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001278172.3:c.140-5540T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407121.1:c.185-5540T>C - intron variant - [Sequence Ontology: SO:0001627]
NR_103459.3:n.406T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001035512.3:c.252T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001035513.3:c.195T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407115.1:c.474T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407116.1:c.297T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407117.1:c.291T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407118.1:c.246T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407119.1:c.243T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407120.1:c.243T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_003001.5:c.354T>C - 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
SCV000698138	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (May 25, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000886092	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Feb 13, 2018)	germline	clinical testing	Citation Link,
SCV004700891	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jan 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698138

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(May 25, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000886092

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Benign
(Feb 13, 2018)

germline

clinical testing

Citation Link,

SCV004700891

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Benign
(Jan 1, 2024)

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, SCV000698138.1

#	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 SDHC c.354T>C (p.Phe118Phe) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant effect on splicing and the creation of two ESE binding sites, however, these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 162/121412 (1 homozygote, 1/749, frequency: 0.001334), predominantly observed in the African cohort, 159/10406 (1 homozygote, 1/65, frequency: 0.01528), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic SDHC variant of 1/5000000 (0.0000002). Therefore, suggesting this variant is a common polymorphism found in population(s) of African origin. In addition, reputable clinical laboratories cite the variant as "benign." Therefore, the variant of interest 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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000886092.1

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004700891.9

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

Description

SDHC: BP4, BP7, 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		1	not provided	not provided	not provided

Last Updated: Jan 13, 2025

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