19-10093467-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_031917.3(ANGPTL6):c.1104C>T(p.Pro368=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00899 in 1,614,224 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0063 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0093 ( 82 hom. )
Consequence
ANGPTL6
NM_031917.3 synonymous
NM_031917.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.00
Genes affected
ANGPTL6 (HGNC:23140): (angiopoietin like 6) Predicted to enable signaling receptor binding activity. Predicted to be involved in angiogenesis and cell differentiation. Located in extracellular exosome. Part of collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 19-10093467-G-A is Benign according to our data. Variant chr19-10093467-G-A is described in ClinVar as [Benign]. Clinvar id is 778156.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL6 | NM_031917.3 | c.1104C>T | p.Pro368= | synonymous_variant | 5/6 | ENST00000253109.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL6 | ENST00000253109.5 | c.1104C>T | p.Pro368= | synonymous_variant | 5/6 | 1 | NM_031917.3 | P1 | |
ANGPTL6 | ENST00000592641.5 | c.1104C>T | p.Pro368= | synonymous_variant | 5/6 | 1 | P1 | ||
ANGPTL6 | ENST00000589181.5 | c.984C>T | p.Pro328= | synonymous_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00633 AC: 963AN: 152228Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00694 AC: 1746AN: 251448Hom.: 15 AF XY: 0.00684 AC XY: 929AN XY: 135908
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GnomAD4 exome AF: 0.00927 AC: 13550AN: 1461878Hom.: 82 Cov.: 31 AF XY: 0.00901 AC XY: 6550AN XY: 727240
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GnomAD4 genome AF: 0.00632 AC: 963AN: 152346Hom.: 9 Cov.: 32 AF XY: 0.00591 AC XY: 440AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | ANGPTL6: BP4, BP7, BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at