NM_000077.5(CDKN2A):c.150+37G>C AND Melanoma-pancreatic cancer syndrome

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Apr 20, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000411071.14

Allele description [Variation Report for NM_000077.5(CDKN2A):c.150+37G>C]

NM_000077.5(CDKN2A):c.150+37G>C

Gene:

CDKN2A:cyclin dependent kinase inhibitor 2A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p21.3

Genomic location:

Preferred name:

NM_000077.5(CDKN2A):c.150+37G>C

Other names:

IVS1+37G>C

HGVS:

NC_000009.12:g.21974641C>G
NG_007485.1:g.24851G>C
NM_000077.5:c.150+37G>CMANE SELECT
NM_001195132.2:c.150+37G>C
NM_001363763.2:c.-3-3433G>C
NM_058195.4:c.194-3433G>C
NM_058197.5:c.187G>C
NP_478104.2:p.Gly63Arg
NP_478104.2:p.Gly63Arg
LRG_11t1:c.150+37G>C
LRG_11t2:c.194-3433G>C
LRG_11:g.24851G>C
NC_000009.11:g.21974640C>G
NM_000077.4:c.150+37G>C
NM_001195132.1:c.150+37G>C
NM_058195.3:c.194-3433G>C
NM_058197.4:c.187G>C
p.G63R

Protein change:

G63R

Links:

dbSNP: rs45456595

NCBI 1000 Genomes Browser:

rs45456595

Molecular consequence:

NM_000077.5:c.150+37G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001195132.2:c.150+37G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001363763.2:c.-3-3433G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_058195.4:c.194-3433G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_058197.5:c.187G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Melanoma-pancreatic cancer syndrome
Identifiers:: MONDO: MONDO:0011713; MedGen: C1838547; Orphanet: 404560; OMIM: 606719

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000488766	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Jun 20, 2016)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 22703879, 22368299, 26775776, 25780468, 24728327, 22292911 Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV001137780	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV004018566	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Apr 20, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000488766

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Jun 20, 2016)

unknown

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV001137780

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV004018566

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Benign
(Apr 20, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

PubMed [citation]

PMID:: 22703879
PMCID:: PMC3397257

CDKN2A is the main susceptibility gene in Italian pancreatic cancer families.

Ghiorzo P, Fornarini G, Sciallero S, Battistuzzi L, Belli F, Bernard L, Bonelli L, Borgonovo G, Bruno W, De Cian F, Decensi A, Filauro M, Faravelli F, Gozza A, Gargiulo S, Mariette F, Nasti S, Pastorino L, Queirolo P, Savarino V, Varesco L, Scarrà GB; et al.

J Med Genet. 2012 Mar;49(3):164-70. doi: 10.1136/jmedgenet-2011-100281.

PubMed [citation]

PMID:: 22368299

See all PubMed Citations (6)

Details of each submission

From Counsyl, SCV000488766.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV001137780.1

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

From Myriad Genetics, Inc., SCV004018566.1

#	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 benign. This variant is intronic and is not expected to impact mRNA splicing.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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