rs2515488

Variant names:

• chr8-6545485-A-C
• rs2515488
• NM_024596.5:c.2214+45556A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-6545485-A-C
• chr8-6545485-A-T

Variant summary

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

The NM_001410916.1(MCPH1):​c.*3A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,116 control chromosomes in the GnomAD database, including 18,809 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 0.49 (18809 hom., cov: 33)
• Consequence: MCPH1 NM_001410916.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001410916.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCPH1	NM_024596.5	MANE Select	c.2214+45556A>C		intron	N/A	NP_078872.3	Q8NEM0-1
	ANGPT2	NM_001118887.2	MANE Select	c.289-12998T>G		intron	N/A	NP_001112359.1	O15123-3
	MCPH1	NM_001410916.1		c.*3A>C		3_prime_UTR	Exon 13 of 13	NP_001397845.1	A0A8I5KZ89

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCPH1	ENST00000344683.10	TSL:1 MANE Select	c.2214+45556A>C		intron	N/A	ENSP00000342924.5	Q8NEM0-1
	ANGPT2	ENST00000629816.3	TSL:1 MANE Select	c.289-12998T>G		intron	N/A	ENSP00000486858.2	O15123-3
	ANGPT2	ENST00000325203.9	TSL:1	c.289-12998T>G		intron	N/A	ENSP00000314897.5	O15123-1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75154 AN: 151998 Hom.: 18773 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.495 AC: 75240 AN: 152116 Hom.: 18809 Cov.: 33 AF XY: 0.495 AC XY: 36852 AN XY: 74378

African (AFR) AF: 0.573 AC: 23769 AN: 41488

American (AMR) AF: 0.476 AC: 7278 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2627 AN: 5188

South Asian (SAS) AF: 0.541 AC: 2607 AN: 4816

European-Finnish (FIN) AF: 0.448 AC: 4732 AN: 10570

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31213 AN: 67980

Other (OTH) AF: 0.506 AC: 1069 AN: 2114

Alfa AF: 0.477 Hom.: 24402

Bravo AF: 0.497

Asia WGS AF: 0.544 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.82
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2515488; hg19: chr8-6403006;