chr20-890327-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015985.4(ANGPT4):c.351G>A(p.Glu117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,613,562 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00062 ( 10 hom. )
Consequence
ANGPT4
NM_015985.4 synonymous
NM_015985.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.65
Genes affected
ANGPT4 (HGNC:487): (angiopoietin 4) Angiopoietins are proteins with important roles in vascular development and angiogenesis. All angiopoietins bind with similar affinity to an endothelial cell-specific tyrosine-protein kinase receptor. The mechanism by which they contribute to angiogenesis is thought to involve regulation of endothelial cell interactions with supporting perivascular cells. The protein encoded by this gene functions as an agonist and is an angiopoietin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 20-890327-C-T is Benign according to our data. Variant chr20-890327-C-T is described in ClinVar as [Benign]. Clinvar id is 710866.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.64 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00588 (896/152294) while in subpopulation AFR AF= 0.0202 (840/41556). AF 95% confidence interval is 0.0191. There are 6 homozygotes in gnomad4. There are 430 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPT4 | NM_015985.4 | c.351G>A | p.Glu117= | synonymous_variant | 2/9 | ENST00000381922.5 | |
ANGPT4 | NM_001322809.2 | c.351G>A | p.Glu117= | synonymous_variant | 2/8 | ||
ANGPT4 | XM_011529239.4 | c.310-1888G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPT4 | ENST00000381922.5 | c.351G>A | p.Glu117= | synonymous_variant | 2/9 | 1 | NM_015985.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00583 AC: 887AN: 152176Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00153 AC: 384AN: 250868Hom.: 2 AF XY: 0.00107 AC XY: 145AN XY: 135632
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GnomAD4 exome AF: 0.000618 AC: 903AN: 1461268Hom.: 10 Cov.: 32 AF XY: 0.000512 AC XY: 372AN XY: 726948
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GnomAD4 genome ? AF: 0.00588 AC: 896AN: 152294Hom.: 6 Cov.: 32 AF XY: 0.00577 AC XY: 430AN XY: 74470
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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 | Invitae | Apr 20, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at