rs373953435

Variant names:

• chr10-13171215-C-G
• rs373953435
• NM_018518.5:c.301C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-13171215-C-G
• chr10-13171215-C-T

Variant summary

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

The NM_018518.5(MCM10):​c.301C>G​(p.Leu101Val) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MCM10 NM_018518.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

Genes affected

MCM10 (HGNC:18043): (minichromosome maintenance 10 replication initiation factor) The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre-RC) and it may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein can interact with MCM2 and MCM6, as well as with the origin recognition protein ORC2. It is regulated by proteolysis and phosphorylation in a cell cycle-dependent manner. Studies of a similar protein in Xenopus suggest that the chromatin binding of this protein at the onset of DNA replication is after pre-RC assembly and before origin unwinding. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [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=0.04886651).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCM10	NM_018518.5	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20	ENST00000378714.8	NP_060988.3
MCM10	NM_182751.3	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20		NP_877428.1
MCM10	XM_011519538.3	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20		XP_011517840.1
MCM10	XM_047425437.1	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20		XP_047281393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCM10	ENST00000378714.8	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20	1	NM_018518.5	ENSP00000367986.3
MCM10	ENST00000484800.6	c.301C>G	p.Leu101Val	missense_variant	Exon 3 of 20	1		ENSP00000418268.1
MCM10	ENST00000378694.1	c.301C>G	p.Leu101Val	missense_variant	Exon 2 of 18	5		ENSP00000367966.1
MCM10	ENST00000479669.5	c.61C>G	p.Leu21Val	missense_variant	Exon 2 of 3	4		ENSP00000417094.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000399 AC: 1 AN: 250604 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135542

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000884

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.063
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.35
DANN	Benign	0.57
DEOGEN2	Benign	0.018	.;T;T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.021	N
LIST_S2	Benign	0.34	T;T;T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.049	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L;.;L;.
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.47	N;N;N;N
REVEL	Benign	0.0090
Sift	Benign	0.26	T;T;T;T
Sift4G	Benign	1.0	T;D;T;T
Polyphen		0.0010	B;.;B;B
Vest4		0.036
MutPred		0.043		Loss of glycosylation at P104 (P = 0.1336);.;Loss of glycosylation at P104 (P = 0.1336);Loss of glycosylation at P104 (P = 0.1336);
MVP		0.15
MPC		0.10
ClinPred		0.046	T
GERP RS		-0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.026
gMVP		0.043

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

LitVar

Other links and lift over

dbSNP: rs373953435; hg19: chr10-13213215;