chr7-100093055-C-G

Position:

• chr7-100093055-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005916.5(MCM7):​c.2037G>C​(p.Glu679Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MCM7 NM_005916.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.128

Genes affected

MCM7 (HGNC:6950): (minichromosome maintenance complex component 7) The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication. The hexameric protein complex formed by the MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. The MCM complex consisting of this protein and MCM2, 4 and 6 proteins possesses DNA helicase activity, and may act as a DNA unwinding enzyme. Cyclin D1-dependent kinase, CDK4, is found to associate with this protein, and may regulate the binding of this protein with the tumorsuppressor protein RB1/RB. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06219995).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCM7	NM_005916.5	c.2037G>C	p.Glu679Asp	missense_variant	15/15	ENST00000303887.10
MCM7	NM_001278595.2	c.1509G>C	p.Glu503Asp	missense_variant	14/14
MCM7	NM_182776.3	c.1509G>C	p.Glu503Asp	missense_variant	14/14
MCM7	XM_005250348.4	c.1716G>C	p.Glu572Asp	missense_variant	15/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCM7	ENST00000303887.10	c.2037G>C	p.Glu679Asp	missense_variant	15/15	1	NM_005916.5	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 25, 2023

The c.2037G>C (p.E679D) alteration is located in exon 15 (coding exon 15) of the MCM7 gene. This alteration results from a G to C substitution at nucleotide position 2037, causing the glutamic acid (E) at amino acid position 679 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.1
DANN	Benign	0.71
DEOGEN2	Benign	0.049	.;.;.;T
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.82
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.86	D;.;T;D
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.062	T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.065	.;.;.;N
MutationTaster	Benign	1.0	D;D;N
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	0.87	N;.;N;N
REVEL	Benign	0.14
Sift	Benign	1.0	T;.;T;T
Sift4G	Benign	0.78	T;T;T;T
Polyphen		0.0	.;.;.;B
Vest4		0.15
MutPred		0.27		.;.;.;Gain of helix (P = 0.0696);
MVP		0.47
MPC		0.12
ClinPred		0.086	T
GERP RS		-0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.063
gMVP		0.41

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-99690678;