rs2959804

chr8-6611331-A-Gchr8-6611331-A-T

Variant summary

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

The NM_024596.5(MCPH1):c.2215-10123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,212 control chromosomes in the GnomAD database, including 66,900 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 0.94 (66900 hom., cov: 32)
• Consequence: MCPH1 NM_024596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

MCPH1 (HGNC:6954): (microcephalin 1) This gene encodes a DNA damage response protein. The encoded protein may play a role in G2/M checkpoint arrest via maintenance of inhibitory phosphorylation of cyclin-dependent kinase 1. Mutations in this gene have been associated with primary autosomal recessive microcephaly 1 and premature chromosome condensation syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCPH1	NM_024596.5	c.2215-10123A>G		intron_variant		ENST00000344683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCPH1	ENST00000344683.10	c.2215-10123A>G		intron_variant		1	NM_024596.5	P1

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142257 AN: 152094 Hom.: 66866 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.935 AC: 142349 AN: 152212 Hom.: 66900 Cov.: 32 AF XY: 0.931 AC XY: 69264 AN XY: 74398

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.935

Alfa AF: 0.945 Hom.: 9153

Bravo AF: 0.933

Asia WGS AF: 0.795 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.37

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: rs2959804; hg19: chr8-6468852;