19-18388480-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_004864.4(GDF15):c.472C>A(p.Arg158Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000733 in 1,605,616 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 0.00069 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00074 ( 14 hom. )
Consequence
GDF15
NM_004864.4 synonymous
NM_004864.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0440
Genes affected
GDF15 (HGNC:30142): (growth differentiation factor 15) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. The protein is expressed in a broad range of cell types, acts as a pleiotropic cytokine and is involved in the stress response program of cells after cellular injury. Increased protein levels are associated with disease states such as tissue hypoxia, inflammation, acute injury and oxidative stress. [provided by RefSeq, Aug 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 19-18388480-C-A is Benign according to our data. Variant chr19-18388480-C-A is described in ClinVar as [Benign]. Clinvar id is 744604.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.044 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000737 (1072/1453632) while in subpopulation EAS AF= 0.0242 (957/39518). AF 95% confidence interval is 0.0229. There are 14 homozygotes in gnomad4_exome. There are 519 alleles in male gnomad4_exome subpopulation. Median coverage is 36. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.472C>A | p.Arg158Arg | synonymous_variant | Exon 2 of 2 | 1 | NM_004864.4 | ENSP00000252809.3 | ||
GDF15 | ENST00000595973.3 | c.472C>A | p.Arg158Arg | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000470531.3 | |||
GDF15 | ENST00000597765.2 | c.472C>A | p.Arg158Arg | synonymous_variant | Exon 3 of 3 | 4 | ENSP00000469819.2 | |||
GDF15 | ENST00000594925.1 | n.290C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000691 AC: 105AN: 151864Hom.: 2 Cov.: 33
GnomAD3 genomes
AF:
AC:
105
AN:
151864
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.00145 AC: 326AN: 225560Hom.: 5 AF XY: 0.00129 AC XY: 162AN XY: 125520
GnomAD3 exomes
AF:
AC:
326
AN:
225560
Hom.:
AF XY:
AC XY:
162
AN XY:
125520
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000737 AC: 1072AN: 1453632Hom.: 14 Cov.: 36 AF XY: 0.000718 AC XY: 519AN XY: 723240
GnomAD4 exome
AF:
AC:
1072
AN:
1453632
Hom.:
Cov.:
36
AF XY:
AC XY:
519
AN XY:
723240
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: 0.000691 AC: 105AN: 151984Hom.: 2 Cov.: 33 AF XY: 0.000861 AC XY: 64AN XY: 74310
GnomAD4 genome
AF:
AC:
105
AN:
151984
Hom.:
Cov.:
33
AF XY:
AC XY:
64
AN XY:
74310
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
25
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Sep 19, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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