NM_144670.6(A2ML1):c.196C>T (p.Leu66=) AND not specified

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Feb 20, 2022
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:: RCV000210521.7

Allele description [Variation Report for NM_144670.6(A2ML1):c.196C>T (p.Leu66=)]

NM_144670.6(A2ML1):c.196C>T (p.Leu66=)

Genes:

A2ML1-AS1:A2ML1 antisense RNA 1 [Gene - HGNC]
A2ML1:alpha-2-macroglobulin like 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_144670.6(A2ML1):c.196C>T (p.Leu66=)

HGVS:

NC_000012.12:g.8823315C>T
NG_042857.1:g.5844C>T
NM_144670.6:c.196C>TMANE SELECT
NP_653271.3:p.Leu66=
NC_000012.11:g.8975911C>T
NM_144670.3:c.196C>T
NM_144670.4:c.196C>T
NM_144670.5:c.196C>T
NM_144670.6:c.196C>T

Links:

dbSNP: rs185519272

NCBI 1000 Genomes Browser:

rs185519272

Molecular consequence:

NM_144670.6:c.196C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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CLNK cytokine dependent hematopoietic cell linker [Homo sapiens]
CLNK cytokine dependent hematopoietic cell linker [Homo sapiens]
Gene ID:116449

Gene
Gene Links for GEO Profiles (Select 69326025) (1)
Gene
Chronic lymphocytic leukemia response to antisense Bcl-2 inhibitor SPC2996: peri...
Chronic lymphocytic leukemia response to antisense Bcl-2 inhibitor SPC2996: peripheral blood
Accession: GDS4284

GEO DataSets
Related DataSets for GEO Profiles (Select 86351679) (1)
GEO DataSets
Conserved Domain Links for Protein (Select 62901109) (1)
Conserved Domains

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000714202	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jul 22, 2017)	germline	clinical testing	Citation Link,
SCV001362975	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Aug 30, 2019)	germline	clinical testing	Citation Link,
SCV002721589	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 20, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000714202

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jul 22, 2017)

germline

clinical testing

Citation Link,

SCV001362975

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Aug 30, 2019)

germline

clinical testing

Citation Link,

SCV002721589

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 20, 2022)

germline

clinical testing

Citation Link

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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 GeneDx, SCV000714202.1

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362975.1

#	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 Ambry Genetics, SCV002721589.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Oct 13, 2024

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