12-57755548-G-C

Variant names:

• chr12-57755548-G-C
• rs1377105251
• NM_138396.6:c.20G>C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_138396.6(MARCHF9):​c.20G>C​(p.Arg7Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000878 in 1,139,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R7L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 8.8e-7 (0 hom.)
• Consequence: MARCHF9 NM_138396.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79
• Publications: 0 publications found

Genes affected

MARCHF9 (HGNC:25139): (membrane associated ring-CH-type finger 9) MARCH9 is a member of the MARCH family of membrane-bound E3 ubiquitin ligases (EC 6.3.2.19). MARCH enzymes add ubiquitin (see MIM 191339) to target lysines in substrate proteins, thereby signaling their vesicular transport between membrane compartments. MARCH9 induces internalization of several membrane glycoproteins and directs them to the endosomal compartment (Bartee et al., 2004 [PubMed 14722266]; Hoer et al., 2007 [PubMed 17174307]).[supplied by OMIM, Apr 2010]

CDK4 (HGNC:1773): (cyclin dependent kinase 4) The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is highly similar to the gene products of S. cerevisiae cdc28 and S. pombe cdc2. It is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression. The activity of this kinase is restricted to the G1-S phase, which is controlled by the regulatory subunits D-type cyclins and CDK inhibitor p16(INK4a). This kinase was shown to be responsible for the phosphorylation of retinoblastoma gene product (Rb). Mutations in this gene as well as in its related proteins including D-type cyclins, p16(INK4a) and Rb were all found to be associated with tumorigenesis of a variety of cancers. Multiple polyadenylation sites of this gene have been reported. [provided by RefSeq, Jul 2008]

CDK4 Gene-Disease associations (from GenCC):

• melanoma, cutaneous malignant, susceptibility to, 3

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33065265).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138396.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCHF9	NM_138396.6	MANE Select	c.20G>C	p.Arg7Pro	missense	Exon 1 of 4	NP_612405.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCHF9	ENST00000266643.6	TSL:1 MANE Select	c.20G>C	p.Arg7Pro	missense	Exon 1 of 4	ENSP00000266643.5	Q86YJ5-1
	CDK4	ENST00000552862.1	TSL:3	c.-20+384C>G		intron	N/A	ENSP00000446763.1	F8W1L8
	MARCHF9	ENST00000552279.1	TSL:2	n.-180G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 8.78e-7 AC: 1 AN: 1139228 Hom.: 0 Cov.: 30 AF XY: 0.00000179 AC XY: 1 AN XY: 559170

African (AFR) AF: 0.00 AC: 0 AN: 22598

American (AMR) AF: 0.00 AC: 0 AN: 18230

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17064

East Asian (EAS) AF: 0.00 AC: 0 AN: 19622

South Asian (SAS) AF: 0.00 AC: 0 AN: 57796

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24164

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2926

European-Non Finnish (NFE) AF: 0.00000107 AC: 1 AN: 934000

Other (OTH) AF: 0.00 AC: 0 AN: 42828

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
BayesDel_addAF	Benign	-0.073	T
BayesDel_noAF	Benign	-0.34
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.042	T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.092
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.56	T
M_CAP	Benign	0.052	D
MetaRNN	Benign	0.33	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.0	L
PhyloP100		4.8
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-0.33	N
REVEL	Benign	0.21
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.10	T
Polyphen		0.99	D
Vest4		0.33
MutPred		0.37		Loss of MoRF binding (P = 9e-04)
MVP		0.41
MPC		2.7
ClinPred		0.88	D
GERP RS		2.2
PromoterAI		0.15	Neutral
Varity_R		0.33
gMVP		0.57
Mutation Taster		=54/46	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1377105251; hg19: chr12-58149331;