NC_000012.11:g.(?_57534470)_(58190366_?)dup AND Familial melanoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 30, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003119257.4

Allele description [Variation Report for NC_000012.11:g.(?_57534470)_(58190366_?)dup]

NC_000012.11:g.(?_57534470)_(58190366_?)dup

Genes:

AGAP2:ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 [Gene - OMIM - HGNC]
DDIT3:DNA damage inducible transcript 3 [Gene - OMIM - HGNC]
EEF1AKMT3:EEF1A lysine methyltransferase 3 [Gene - OMIM - HGNC]
GLI1:GLI family zinc finger 1 [Gene - OMIM - HGNC]
LRP1:LDL receptor related protein 1 [Gene - OMIM - HGNC]
NDUFA4L2:NDUFA4 mitochondrial complex associated like 2 [Gene - HGNC]
OS9:OS9 endoplasmic reticulum lectin [Gene - OMIM - HGNC]
R3HDM2:R3H domain containing 2 [Gene - OMIM - HGNC]
ARHGAP9:Rho GTPase activating protein 9 [Gene - OMIM - HGNC]
ARHGEF25:Rho guanine nucleotide exchange factor 25 [Gene - OMIM - HGNC]
STAC3:SH3 and cysteine rich domain 3 [Gene - OMIM - HGNC]
TSFM:Ts translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
B4GALNT1:beta-1,4-N-acetyl-galactosaminyltransferase 1 [Gene - OMIM - HGNC]
CDK4:cyclin dependent kinase 4 [Gene - OMIM - HGNC]
CYP27B1:cytochrome P450 family 27 subfamily B member 1 [Gene - OMIM - HGNC]
DTX3:deltex E3 ubiquitin ligase 3 [Gene - OMIM - HGNC]
DCTN2:dynactin subunit 2 [Gene - OMIM - HGNC]
INHBC:inhibin subunit beta C [Gene - OMIM - HGNC]
INHBE:inhibin subunit beta E [Gene - OMIM - HGNC]
KIF5A:kinesin family member 5A [Gene - OMIM - HGNC]
MARCHF9:membrane associated ring-CH-type finger 9 [Gene - OMIM - HGNC]
MARS1:methionyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
MBD6:methyl-CpG binding domain protein 6 [Gene - OMIM - HGNC]
METTL1:methyltransferase 1, tRNA methylguanosine [Gene - OMIM - HGNC]
MIR616:microRNA 616 [Gene - OMIM - HGNC]
NXPH4:neurexophilin 4 [Gene - OMIM - HGNC]
PIP4K2C:phosphatidylinositol-5-phosphate 4-kinase type 2 gamma [Gene - OMIM - HGNC]
SHMT2:serine hydroxymethyltransferase 2 [Gene - OMIM - HGNC]
TSPAN31:tetraspanin 31 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

12q13.3-14.1

Genomic location:

Chr12: 57534470 - 58190366 (on Assembly GRCh37)

Preferred name:

NC_000012.11:g.(?_57534470)_(58190366_?)dup

HGVS:

NC_000012.11:g.(?_57534470)_(58190366_?)dup

Condition(s)

Name:: Familial melanoma
Synonyms:: Hereditary melanoma; Hereditary cutaneous melanoma
Identifiers:: MONDO: MONDO:0018961; MedGen: C1512419

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790222	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 30, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790222

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 30, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003790222.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the CDK4 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with CDK4-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Jan 13, 2025

ClinVar

Relating variation to medicine