19-10096138-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_031917.3(ANGPTL6):c.426C>T(p.Arg142=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,404,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
ANGPTL6
NM_031917.3 synonymous
NM_031917.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.30
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 19-10096138-G-A is Benign according to our data. Variant chr19-10096138-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 738121.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.3 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL6 | NM_031917.3 | c.426C>T | p.Arg142= | synonymous_variant | 2/6 | ENST00000253109.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL6 | ENST00000253109.5 | c.426C>T | p.Arg142= | synonymous_variant | 2/6 | 1 | NM_031917.3 | P1 | |
ANGPTL6 | ENST00000592641.5 | c.426C>T | p.Arg142= | synonymous_variant | 2/6 | 1 | P1 | ||
ANGPTL6 | ENST00000589181.5 | c.426C>T | p.Arg142= | synonymous_variant | 1/5 | 5 | |||
ANGPTL6 | ENST00000586910.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151674Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
2
AN:
151674
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000144 AC: 18AN: 1252622Hom.: 0 Cov.: 31 AF XY: 0.0000130 AC XY: 8AN XY: 615258
GnomAD4 exome
AF:
AC:
18
AN:
1252622
Hom.:
Cov.:
31
AF XY:
AC XY:
8
AN XY:
615258
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151674Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74090
GnomAD4 genome
AF:
AC:
2
AN:
151674
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
74090
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at