NM_001146.5:c.298-49084T>G

Variant names:

• chr8-107396181-A-C
• rs4268102
• NM_001146.5:c.298-49084T>G

Variant summary

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

The NM_001146.5(ANGPT1):​c.298-49084T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,996 control chromosomes in the GnomAD database, including 8,223 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 0.31 (8223 hom., cov: 32)
• Consequence: ANGPT1 NM_001146.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 6 publications found

Genes affected

ANGPT1 (HGNC:484): (angiopoietin 1) This gene encodes a secreted glycoprotein that belongs to the angiopoietin family. Members of this family play important roles in vascular development and angiogenesis. All angiopoietins bind with similar affinity to an endothelial cell-specific tyrosine-protein kinase receptor. The protein encoded by this gene is a secreted glycoprotein that activates the receptor by inducing its tyrosine phosphorylation. It plays a critical role in mediating reciprocal interactions between the endothelium and surrounding matrix and mesenchyme and inhibits endothelial permeability. The protein also contributes to blood vessel maturation and stability, and may be involved in early development of the heart. Mutations in this gene are associated with hereditary angioedema. [provided by RefSeq, Aug 2020]

ANGPT1 Gene-Disease associations (from GenCC):

• glaucoma

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• primary congenital glaucoma

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• angioedema, hereditary, 5

  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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146.5. 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
	ANGPT1	NM_001146.5	MANE Select	c.298-49084T>G		intron	N/A	NP_001137.2
	ANGPT1	NM_001199859.3		c.298-49084T>G		intron	N/A	NP_001186788.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANGPT1	ENST00000517746.6	TSL:1 MANE Select	c.298-49084T>G		intron	N/A	ENSP00000428340.1
	ANGPT1	ENST00000297450.7	TSL:1	c.298-49084T>G		intron	N/A	ENSP00000297450.3
	ANGPT1	ENST00000520033.1	TSL:4	c.-24-49084T>G		intron	N/A	ENSP00000428908.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46440 AN: 151878 Hom.: 8207 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.306 AC: 46493 AN: 151996 Hom.: 8223 Cov.: 32 AF XY: 0.306 AC XY: 22764 AN XY: 74324

African (AFR) AF: 0.472 AC: 19545 AN: 41416

American (AMR) AF: 0.282 AC: 4307 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3003 AN: 5154

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4818

European-Finnish (FIN) AF: 0.198 AC: 2098 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14870 AN: 67952

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.248 Hom.: 22372

Bravo AF: 0.321

Asia WGS AF: 0.399 AC: 1383 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.54
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4268102; hg19: chr8-108408409;