NM_024596.5:c.2214+37371T>C

Variant names:

• chr8-6537300-T-C
• rs2442598
• NM_024596.5:c.2214+37371T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024596.5(MCPH1):​c.2214+37371T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,888 control chromosomes in the GnomAD database, including 38,387 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 0.71 (38387 hom., cov: 30)
• Consequence: MCPH1 NM_024596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 24 publications found

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]

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]

ANGPT2 Gene-Disease associations (from GenCC):

• lymphatic malformation 10

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024596.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCPH1	NM_024596.5	MANE Select	c.2214+37371T>C		intron	N/A	NP_078872.3
	ANGPT2	NM_001118887.2	MANE Select	c.289-4813A>G		intron	N/A	NP_001112359.1
	MCPH1	NM_001322042.2		c.2214+37371T>C		intron	N/A	NP_001308971.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCPH1	ENST00000344683.10	TSL:1 MANE Select	c.2214+37371T>C		intron	N/A	ENSP00000342924.5
	ANGPT2	ENST00000629816.3	TSL:1 MANE Select	c.289-4813A>G		intron	N/A	ENSP00000486858.2
	ANGPT2	ENST00000325203.9	TSL:1	c.289-4813A>G		intron	N/A	ENSP00000314897.5

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107560 AN: 151770 Hom.: 38349 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.709 AC: 107647 AN: 151888 Hom.: 38387 Cov.: 30 AF XY: 0.704 AC XY: 52237 AN XY: 74214

African (AFR) AF: 0.729 AC: 30196 AN: 41394

American (AMR) AF: 0.781 AC: 11926 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2457 AN: 3464

East Asian (EAS) AF: 0.521 AC: 2683 AN: 5150

South Asian (SAS) AF: 0.625 AC: 3004 AN: 4804

European-Finnish (FIN) AF: 0.656 AC: 6908 AN: 10536

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48229 AN: 67944

Other (OTH) AF: 0.728 AC: 1537 AN: 2112

Alfa AF: 0.714 Hom.: 62864

Bravo AF: 0.716

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.25
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2442598; hg19: chr8-6394821;