20-5955177-A-T

Variant names:

• chr20-5955177-A-T
• rs781597825
• NM_032485.6:c.412A>T

Variant summary

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

The NM_032485.6(MCM8):​c.412A>T​(p.Ile138Leu) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I138V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MCM8 NM_032485.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

Genes affected

MCM8 (HGNC:16147): (minichromosome maintenance 8 homologous recombination repair factor) 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 mini-chromosome maintenance proteins is a key component of the pre-replication complex and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein contains the central domain that is conserved among the mini-chromosome maintenance proteins. The encoded protein may interact with other mini-chromosome maintenance proteins and play a role in DNA replication. This gene may be associated with length of reproductive lifespan and menopause. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2013]

ENSG00000286235 (HGNC:):

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=0.04230377).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCM8	NM_032485.6	c.412A>T	p.Ile138Leu	missense_variant	Exon 5 of 19	ENST00000610722.4	NP_115874.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCM8	ENST00000610722.4	c.412A>T	p.Ile138Leu	missense_variant	Exon 5 of 19	1	NM_032485.6	ENSP00000478141.1
ENSG00000286235	ENST00000652720.1	c.412A>T	p.Ile138Leu	missense_variant	Exon 5 of 24			ENSP00000498784.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.064
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.8
DANN	Benign	0.55
DEOGEN2	Benign	0.015	.;T;.;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.55	T;T;T;.;T
M_CAP	Benign	0.0065	T
MetaRNN	Benign	0.042	T;T;T;T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	1.2	L;L;L;L;L
PrimateAI	Benign	0.43	T
PROVEAN	Benign	0.0	N;N;N;.;N
REVEL	Benign	0.087
Sift	Benign	0.70	T;T;T;.;T
Sift4G	Benign	0.82	T;T;T;T;T
Polyphen		0.0	B;B;.;B;B
Vest4		0.26
MutPred		0.45		Gain of disorder (P = 0.1732);Gain of disorder (P = 0.1732);Gain of disorder (P = 0.1732);Gain of disorder (P = 0.1732);Gain of disorder (P = 0.1732);
MVP		0.11
MPC		0.13
ClinPred		0.044	T
GERP RS		-1.0
Varity_R		0.036
gMVP		0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs781597825; hg19: chr20-5935823;