rs2442631

Positions:

• chr8-6511255-C-T

Variant summary

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

The NM_024596.5(MCPH1):​c.2214+11326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,632 control chromosomes in the GnomAD database, including 14,062 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 0.43 (14062 hom., cov: 31)
• Consequence: MCPH1 NM_024596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

ANGPT2 (HGNC:485): (angiopoietin 2) This gene belongs to the angiopoietin family of growth factors. The protein encoded by this gene is an antagonist of angiopoietin 1, and both angiopoietin 1 and angiopoietin 2 are ligands for the endothelial TEK receptor tyrosine kinase. Angiopoietin 2 is upregulated in multiple inflammatory diseases and is implicated in the direct control of inflammation-related signaling pathways. The encoded protein affects angiogenesis during embryogenesis and tumorigenesis, disrupts the vascular remodeling ability of angiopoietin 1, and may induce endothelial cell apoptosis. This gene serves a prognostic biomarker for acute respiratory distress syndrome. [provided by RefSeq, Aug 2020]

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANGPT2	NM_001118887.2	c.1197-2193G>A		intron_variant		ENST00000629816.3
MCPH1	NM_024596.5	c.2214+11326C>T		intron_variant		ENST00000344683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCPH1	ENST00000344683.10	c.2214+11326C>T		intron_variant		1	NM_024596.5	P1
ANGPT2	ENST00000629816.3	c.1197-2193G>A		intron_variant		1	NM_001118887.2	P4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64718 AN: 151518 Hom.: 14061 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.427 AC: 64744 AN: 151632 Hom.: 14062 Cov.: 31 AF XY: 0.422 AC XY: 31249 AN XY: 74096

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.448

Alfa AF: 0.448 Hom.: 18568

Bravo AF: 0.422

Asia WGS AF: 0.290 AC: 1008 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.46

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: rs2442631; hg19: chr8-6368776;