rs4815879

chr20-5968888-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032485.6(MCM8):c.1223+863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,264 control chromosomes in the GnomAD database, including 410 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.068 (410 hom., cov: 32)
• Consequence: MCM8 NM_032485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCM8	NM_032485.6	c.1223+863G>A		intron_variant		ENST00000610722.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCM8	ENST00000610722.4	c.1223+863G>A		intron_variant		1	NM_032485.6	P1

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10357 AN: 152146 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.0580

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0680 AC: 10354 AN: 152264 Hom.: 410 Cov.: 32 AF XY: 0.0675 AC XY: 5026 AN XY: 74460

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0961

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0878 Hom.: 939

Bravo AF: 0.0662

Asia WGS AF: 0.0610 AC: 212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.5
Dann	Benign	0.53

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: rs4815879; hg19: chr20-5949534;