10-13172438-A-T

Variant names:

• chr10-13172438-A-T
• NM_018518.5:c.412A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_018518.5(MCM10):​c.412A>T​(p.Ile138Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: MCM10 NM_018518.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10364708).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCM10	NM_018518.5	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20	ENST00000378714.8	NP_060988.3
MCM10	NM_182751.3	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20		NP_877428.1
MCM10	XM_011519538.3	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20		XP_011517840.1
MCM10	XM_047425437.1	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20		XP_047281393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCM10	ENST00000378714.8	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20	1	NM_018518.5	ENSP00000367986.3
MCM10	ENST00000484800.6	c.412A>T	p.Ile138Phe	missense_variant	Exon 4 of 20	1		ENSP00000418268.1
MCM10	ENST00000378694.1	c.412A>T	p.Ile138Phe	missense_variant	Exon 3 of 18	5		ENSP00000367966.1
MCM10	ENST00000479669.5	c.172A>T	p.Ile58Phe	missense_variant	Exon 3 of 3	4		ENSP00000417094.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1461868 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 727232

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000629

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.026	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	15
DANN	Benign	0.95
DEOGEN2	Benign	0.16	.;T;T;.
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.47	N
LIST_S2	Benign	0.76	T;T;T;T
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.10	T;T;T;T
MetaSVM	Benign	-0.81	T
MutationAssessor	Uncertain	2.3	M;.;M;.
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-1.0	N;D;N;N
REVEL	Benign	0.10
Sift	Benign	0.041	D;D;D;D
Sift4G	Uncertain	0.029	D;D;T;D
Polyphen		0.92	P;.;P;P
Vest4		0.31
MutPred		0.098		Gain of methylation at K139 (P = 0.0848);.;Gain of methylation at K139 (P = 0.0848);Gain of methylation at K139 (P = 0.0848);
MVP		0.49
MPC		0.33
ClinPred		0.39	T
GERP RS		1.9
Varity_R		0.11
gMVP		0.099

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: chr10-13214438;