rs2916716
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001118887.2(ANGPT2):c.*3387T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 723,324 control chromosomes in the GnomAD database, including 33,836 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.24 ( 5672 hom., cov: 32)
Exomes 𝑓: 0.30 ( 28164 hom. )
Consequence
ANGPT2
NM_001118887.2 3_prime_UTR
NM_001118887.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.137
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 8-6499714-A-T is Benign according to our data. Variant chr8-6499714-A-T is described in ClinVar as [Benign]. Clinvar id is 1262416.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPT2 | NM_001118887.2 | c.*3387T>A | 3_prime_UTR_variant | 9/9 | ENST00000629816.3 | ||
MCPH1 | NM_024596.5 | c.2137-138A>T | intron_variant | ENST00000344683.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPT2 | ENST00000629816.3 | c.*3387T>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001118887.2 | P4 | ||
MCPH1 | ENST00000344683.10 | c.2137-138A>T | intron_variant | 1 | NM_024596.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.241 AC: 36566AN: 151974Hom.: 5676 Cov.: 32
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GnomAD4 exome AF: 0.299 AC: 170966AN: 571232Hom.: 28164 Cov.: 7 AF XY: 0.299 AC XY: 91479AN XY: 305510
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GnomAD4 genome ? AF: 0.240 AC: 36546AN: 152092Hom.: 5672 Cov.: 32 AF XY: 0.237 AC XY: 17596AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at