NM_022455.5(NSD1):c.7908C>T (p.Leu2636=) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Aug 21, 2015
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:: RCV000146954.18

Allele description [Variation Report for NM_022455.5(NSD1):c.7908C>T (p.Leu2636=)]

NM_022455.5(NSD1):c.7908C>T (p.Leu2636=)

Gene:

NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_022455.5(NSD1):c.7908C>T (p.Leu2636=)

HGVS:

NC_000005.10:g.177295276C>T
NG_009821.1:g.167198C>T
NM_001365684.2:c.7035C>T
NM_001409301.1:c.7908C>T
NM_001409302.1:c.7908C>T
NM_001409303.1:c.7908C>T
NM_001409304.1:c.7488C>T
NM_001409305.1:c.7155C>T
NM_001409306.1:c.7146C>T
NM_001409307.1:c.7146C>T
NM_001409308.1:c.7035C>T
NM_001409309.1:c.6786C>T
NM_022455.5:c.7908C>TMANE SELECT
NM_172349.5:c.7035C>T
NP_001352613.2:p.Leu2345=
NP_001396230.1:p.Leu2636=
NP_001396231.1:p.Leu2636=
NP_001396232.1:p.Leu2636=
NP_001396233.1:p.Leu2496=
NP_001396234.1:p.Leu2385=
NP_001396235.1:p.Leu2382=
NP_001396236.1:p.Leu2382=
NP_001396237.1:p.Leu2345=
NP_001396238.1:p.Leu2262=
NP_071900.2:p.Leu2636=
NP_071900.2:p.Leu2636=
NP_758859.2:p.Leu2345=
LRG_512t1:c.7908C>T
LRG_512:g.167198C>T
LRG_512p1:p.Leu2636=
NC_000005.9:g.176722277C>T
NM_022455.4:c.7908C>T

Links:

dbSNP: rs143159630

Molecular consequence:

NM_001365684.2:c.7035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409301.1:c.7908C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409302.1:c.7908C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409303.1:c.7908C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409304.1:c.7488C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409305.1:c.7155C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409306.1:c.7146C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409307.1:c.7146C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409308.1:c.7035C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409309.1:c.6786C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_022455.5:c.7908C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_172349.5:c.7035C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000194289	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Benign (Feb 8, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000228077	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Aug 21, 2015)	germline	clinical testing	Citation Link,
SCV000513990	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Mar 11, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000194289

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Benign
(Feb 8, 2013)

germline

clinical testing

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

SCV000228077

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Aug 21, 2015)

germline

clinical testing

Citation Link,

SCV000513990

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Mar 11, 2015)

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	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee.

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000194289.1

#	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 Eurofins Ntd Llc (ga), SCV000228077.6

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

From GeneDx, SCV000513990.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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: Jun 20, 2026

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